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Sample records for gromos force-field parameter

  1. Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field.

    Science.gov (United States)

    Margreitter, Christian; Reif, Maria M; Oostenbrink, Chris

    2017-04-15

    In this study, we propose newly derived parameters for phosphate ions in the context of the GROMOS force field parameter sets. The non-bonded parameters used up to now lead to a hydration free energy, which renders the dihydrogen phosphate ion too hydrophobic when compared to experimentally derived values, making a reparametrization of the phosphate moiety necessary. Phosphate species are of great importance in biomolecular simulations not only because of their crucial role in the backbone of nucleic acids but also as they represent one of the most important types of post-translational modifications to protein side-chains and are an integral part in many lipids. Our re-parametrization of the free dihydrogen phosphate (H 2PO 4-) and three derivatives (methyl phosphate, dimethyl phosphate, and phenyl phosphate) leads, in conjunction with the previously updated charged side-chains in the GROMOS parameter set 54A8, to new nucleic acid backbone parameters and a 54A8 version of the widely used GROMOS protein post-translational modification parameter set. © 2017 Wiley Periodicals, Inc.

  2. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

    Energy Technology Data Exchange (ETDEWEB)

    Soares, T. A. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Daura, X. [Universitat Autonoma de Barcelona, InstitucioCatalana de Recerca i Estudis Avancats and Institut de Biotecnologia i Biomedicina (Spain); Oostenbrink, C. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Smith, L. J. [University of Oxford, Oxford Centre for Molecular Sciences, Central Chemistry Laboratory (United Kingdom); Gunsteren, W. F. van [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland)], E-mail: wfvgn@igc.phys.chem.ethz.ch

    2004-12-15

    The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, {sup 3}J{sub NH{alpha}} and {sup 3}J{sub {alpha}}{sub {beta}} coupling constants, and {sup 1}5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone {sup 3}J{sub HN{alpha}}-coupling constants and {sup 1}H- {sup 1}5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain {sup 3}J{sub {alpha}}{sub {beta}}-coupling constants and {sup 1}H- {sup 1}5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the

  3. Supra-Atomic Coarse-Grained GROMOS Force Field for Aliphatic Hydrocarbons in the Liquid Phase.

    Science.gov (United States)

    Eichenberger, Andreas P; Huang, Wei; Riniker, Sereina; van Gunsteren, Wilfred F

    2015-07-14

    A supra-atomic coarse-grained (CG) force field for liquid n-alkanes is presented. The model was calibrated using experimental thermodynamic data and structural as well as energetic properties for 14 n-alkanes as obtained from atomistic fine-grained (FG) simulations of the corresponding hydrocarbons using the GROMOS 45A3 biomolecular force field. A variation of the nonbonded force-field parameters obtained from mapping the FG interactions onto the CG degrees of freedom to fit the density and heat of vaporization to experimental values turned out to be mandatory for a correct reproduction of these data by the CG model, while the bonded force-field parameters for the CG model could be obtained from a Boltzmann-weighted fit with some variations with respect to the corresponding properties from the FG simulations mapped onto the CG degrees of freedom. The model presents 6 different CG bead types, for bead sizes from 2 to 4 distinguishing between terminal and nonterminal beads within an alkane chain (end or middle). It contains different nonbonded Lennard-Jones parameters for the interaction of CG alkanes with CG water. The CG alkane model was further tested by comparing predictions of the excess free energy, the self-diffusion constant, surface tension, isothermal compressibility, heat capacity, thermal expansion coefficient, and shear viscosity for n-alkanes to experimental values. The CG model offers a thermodynamically calibrated basis for the development of CG models of lipids.

  4. A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers.

    Science.gov (United States)

    Hansen, Halvor S; Hünenberger, Philippe H

    2011-04-30

    This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences

  5. Deriving force field parameters for coordination complexes

    DEFF Research Database (Denmark)

    Norrby, Per-Ola; Brandt, Peter

    2001-01-01

    The process of deriving molecular mechanics force fields for coordination complexes is outlined. Force field basics are introduced with an emphasis on special requirements for metal complexes. The review is then focused on how to set up the initial model, define the target, refine the parameters,...

  6. How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

    NARCIS (Netherlands)

    Villa, Alessandra; Fan, Hao; Wassenaar, Tsjerk; Mark, Alan E.

    2007-01-01

    The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ signifi

  7. An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.

    Science.gov (United States)

    Malde, Alpeshkumar K; Zuo, Le; Breeze, Matthew; Stroet, Martin; Poger, David; Nair, Pramod C; Oostenbrink, Chris; Mark, Alan E

    2011-12-13

    The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.

  8. Global optimization of parameters in the reactive force field ReaxFF for SiOH.

    Science.gov (United States)

    Larsson, Henrik R; van Duin, Adri C T; Hartke, Bernd

    2013-09-30

    We have used unbiased global optimization to fit a reactive force field to a given set of reference data. Specifically, we have employed genetic algorithms (GA) to fit ReaxFF to SiOH data, using an in-house GA code that is parallelized across reference data items via the message-passing interface (MPI). Details of GA tuning turn-ed out to be far less important for global optimization efficiency than using suitable ranges within which the parameters are varied. To establish these ranges, either prior knowledge can be used or successive stages of GA optimizations, each building upon the best parameter vectors and ranges found in the previous stage. We have finally arrive-ed at optimized force fields with smaller error measures than those published previously. Hence, this optimization approach will contribute to converting force-field fitting from a specialist task to an everyday commodity, even for the more difficult case of reactive force fields.

  9. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.

    Science.gov (United States)

    Zheng, Suqing; Tang, Qing; He, Jian; Du, Shiyu; Xu, Shaofang; Wang, Chaojie; Xu, Yong; Lin, Fu

    2016-04-25

    Force fields are fundamental to molecular dynamics simulations. However, the incompleteness of force field parameters has been a long-standing problem, especially for metal-related systems. In our previous work, we adopted the Seminario method based on the Hessian matrix to systematically derive the zinc-related force field parameters for AMBER. In this work, in order to further simplify the whole protocol, we have implemented a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.

  10. Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability

    CERN Document Server

    Sakae, Yoshitake

    2013-01-01

    We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of $\\psi$ (N-C$^{\\alpha}$-C-N) and $\\zeta$ (C$^{\\beta}$-C$^{\\alpha}$-C-N) of the backbone dihedral angles. We then performed folding simulations of $\\alpha$-helical and $\\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff99SB force field.

  11. Paramfit: automated optimization of force field parameters for molecular dynamics simulations.

    Science.gov (United States)

    Betz, Robin M; Walker, Ross C

    2015-01-15

    The generation of bond, angle, and torsion parameters for classical molecular dynamics force fields typically requires fitting parameters such that classical properties such as energies and gradients match precalculated quantum data for structures that scan the value of interest. We present a program, Paramfit, distributed as part of the AmberTools software package that automates and extends this fitting process, allowing for simplified parameter generation for applications ranging from single molecules to entire force fields. Paramfit implements a novel combination of a genetic and simplex algorithm to find the optimal set of parameters that replicate either quantum energy or force data. The program allows for the derivation of multiple parameters simultaneously using significantly fewer quantum calculations than previous methods, and can also fit parameters across multiple molecules with applications to force field development. Paramfit has been applied successfully to systems with a sparse number of structures, and has already proven crucial in the development of the Assisted Model Building with Energy Refinement Lipid14 force field.

  12. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

    Science.gov (United States)

    Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian

    2014-11-20

    Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.

  13. A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

    Directory of Open Access Journals (Sweden)

    Giuliano Malloci

    2015-08-01

    Full Text Available We present an on-line database of all-atom force-field parameters and molecular properties of compounds with antimicrobial activity (mostly antibiotics and some beta-lactamase inhibitors. For each compound, we provide the General Amber Force Field parameters for the major species at physiological pH, together with an analysis of properties of interest as extracted from µs-long molecular dynamics simulations in explicit water solution. The properties include number and population of structural clusters, molecular flexibility, hydrophobic and hydrophilic molecular surfaces, the statistics of intraand inter-molecular H-bonds, as well as structural and dynamical properties of solvent molecules within first and second solvation shells. In addition, the database contains several key molecular parameters, such as energy of the frontier molecular orbitals, vibrational properties, rotational constants, atomic partial charges and electric dipole moment, computed by Density Functional Theory. The present database (to our knowledge the first extensive one including dynamical properties is part of a wider project aiming to build-up a database containing structural, physico-chemical and dynamical properties of medicinal compounds using different force-field parameters with increasing level of complexity and reliability. The database is freely accessible at http://www.dsf.unica.it/translocation/db/.

  14. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges

    Science.gov (United States)

    Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D.

    2012-01-01

    Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A “penalty score” is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data. PMID:23145473

  15. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues.

    Science.gov (United States)

    Li, Xinbi; Ponomarev, Sergei Y; Sa, Qina; Sigalovsky, Daniel L; Kaminski, George A

    2013-05-30

    A previously introduced polarizable simulations with second-order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies, and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins.

  16. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

    Science.gov (United States)

    Ponomarev, Sergei Y.; Kaminski, George A.

    2011-01-01

    A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:21743799

  17. Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach.

    Science.gov (United States)

    Várnai, Csilla; Burkoff, Nikolas S; Wild, David L

    2013-12-10

    Maximum Likelihood (ML) optimization schemes are widely used for parameter inference. They maximize the likelihood of some experimentally observed data, with respect to the model parameters iteratively, following the gradient of the logarithm of the likelihood. Here, we employ a ML inference scheme to infer a generalizable, physics-based coarse-grained protein model (which includes Go̅-like biasing terms to stabilize secondary structure elements in room-temperature simulations), using native conformations of a training set of proteins as the observed data. Contrastive divergence, a novel statistical machine learning technique, is used to efficiently approximate the direction of the gradient ascent, which enables the use of a large training set of proteins. Unlike previous work, the generalizability of the protein model allows the folding of peptides and a protein (protein G) which are not part of the training set. We compare the same force field with different van der Waals (vdW) potential forms: a hard cutoff model, and a Lennard-Jones (LJ) potential with vdW parameters inferred or adopted from the CHARMM or AMBER force fields. Simulations of peptides and protein G show that the LJ model with inferred parameters outperforms the hard cutoff potential, which is consistent with previous observations. Simulations using the LJ potential with inferred vdW parameters also outperforms the protein models with adopted vdW parameter values, demonstrating that model parameters generally cannot be used with force fields with different energy functions. The software is available at https://sites.google.com/site/crankite/.

  18. The evaluation and validation of copper (II) force field parameters of the Auxiliary Activity family 9 enzymes

    Science.gov (United States)

    Moses, Vuyani; Tastan Bishop, Özlem; Lobb, Kevin A.

    2017-06-01

    The Auxiliary Activity family 9 (AA9) proteins are Cu2+ coordinating enzymes which are crucial for the early stages of cellulose degradation. In this study, the force field parameters for copper-containing bonds in the Type 1 AA9 protein active site were established and used in a molecular dynamics simulation on a solvated, neutralized system containing an AA9 protein, Cu2+ and a β-cellulose surface. The copper to cellulose interaction was evident during the dynamics, which could also be accelerated by the use of high Cusbnd O van der Waals parameters. The interaction of AA9, Cu2+ and cellulose is described in detail.

  19. Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field

    DEFF Research Database (Denmark)

    Reichert, David E.; Norrby, Per-Ola; Welch, Michael J.

    2001-01-01

    In this work we describe the development of parameters for In(III) and Cu(II) for the AMBER* force field as found in the modeling package MacroModel. These parameters were developed using automated procedures from a combination of crystallographic structures and ab initio calculations. The new pa...... then utilized to examine the conformational effects caused by the conjugation of InDTPA (DTPA = diethylenetriaminepentaacetic acid) and CuDOTA (DOTA 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) to the cyclic octapeptide octreotide....

  20. A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

    Science.gov (United States)

    Zgarbová, Marie; Luque, F Javier; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr

    2012-09-11

    A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA χOL3 parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput.2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches.

  1. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Zhixiong; Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich (Switzerland)

    2015-03-07

    Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

  2. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2.

    Science.gov (United States)

    Lin, Zhixiong; Bachmann, Stephan J; van Gunsteren, Wilfred F

    2015-03-07

    Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

  3. GROMOS polarizable charge-on-spring models for liquid urea: COS/U and COS/U2

    Science.gov (United States)

    Lin, Zhixiong; Bachmann, Stephan J.; van Gunsteren, Wilfred F.

    2015-03-01

    Two one-site polarizable urea models, COS/U and COS/U2, based on the charge-on-spring model are proposed. The models are parametrized against thermodynamic properties of urea-water mixtures in combination with the polarizable COS/G2 and COS/D2 models for liquid water, respectively, and have the same functional form of the inter-atomic interaction function and are based on the same parameter calibration procedure and type of experimental data as used to develop the GROMOS biomolecular force field. Thermodynamic, dielectric, and dynamic properties of urea-water mixtures simulated using the polarizable models are closer to experimental data than using the non-polarizable models. The COS/U and COS/U2 models may be used in biomolecular simulations of protein denaturation.

  4. Determination of best-fit potential parameters for a reactive force field using a genetic algorithm.

    Science.gov (United States)

    Pahari, Poonam; Chaturvedi, Shashank

    2012-03-01

    The ReaxFF interatomic potential, used for organic materials, involves more than 600 adjustable parameters, the best-fit values of which must be determined for different materials. A new method of determining the set of best-fit parameters for specific molecules containing carbon, hydrogen, nitrogen and oxygen is presented, based on a parameter reduction technique followed by genetic algorithm (GA) minimization. This work has two novel features. The first is the use of a parameter reduction technique to determine which subset of parameters plays a significant role for the species of interest; this is necessary to reduce the optimization space to manageable levels. The second is the application of the GA technique to a complex potential (ReaxFF) with a very large number of adjustable parameters, which implies a large parameter space for optimization. In this work, GA has been used to optimize the parameter set to determine best-fit parameters that can reproduce molecular properties to within a given accuracy. As a test problem, the use of the algorithm has been demonstrated for nitromethane and its decomposition products.

  5. Valence state parameters of all transition metal atoms in metalloproteins--development of ABEEMσπ fluctuating charge force field.

    Science.gov (United States)

    Yang, Zhong-Zhi; Wang, Jian-Jiang; Zhao, Dong-Xia

    2014-09-05

    To promote accuracy of the atom-bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc-Zn, Y-Cd, and Lu-Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO-3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy.

  6. Molecular Simulations of Dodecyl-β-maltoside Micelles in Water: Influence of the Headgroup Conformation and Force field Parameters

    Science.gov (United States)

    Abel, Stéphane; Dupradeau, François-Yves; Raman, E. Prabhu; MacKerell, Alexander D.; Marchi, Massimo

    2011-01-01

    This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-Dodecyl-ß-maltoside (C12G2), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size, shape, internal structure and hydration of the C12G2 anomer micelles were thoroughly investigated by molecular dynamics simulations and the results compared with experiments. Additional simulations were also performed with the older CHARMM22 force field for carbohydrates (Kuttel, M. et al. J. Comp. Chem. 2002, 23, 1236-1243). We find that our CHARMM and GLYCAM parameter sets yields similar results in case of properties related to the micelle structure, but differ for other properties such as the headgroup conformation or the micelle hydration. In agreement with experiments, our results show that for all model potentials the β-C12G2 micelles have a more pronounced ellipsoidal shape than those containing α anomers. The computed radius of gyration is 20.2 Å and 25.4 Å for the α- and β-anomer micelles, respectively. Finally, we show that depending on the potential the water translational diffusion of the interfacial water is 7 - 11.5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in α- or β- anomers. PMID:21192681

  7. SpaGrOW—A Derivative-Free Optimization Scheme for Intermolecular Force Field Parameters Based on Sparse Grid Methods

    Directory of Open Access Journals (Sweden)

    Dirk Reith

    2013-09-01

    Full Text Available Molecular modeling is an important subdomain in the field of computational modeling, regarding both scientific and industrial applications. This is because computer simulations on a molecular level are a virtuous instrument to study the impact of microscopic on macroscopic phenomena. Accurate molecular models are indispensable for such simulations in order to predict physical target observables, like density, pressure, diffusion coefficients or energetic properties, quantitatively over a wide range of temperatures. Thereby, molecular interactions are described mathematically by force fields. The mathematical description includes parameters for both intramolecular and intermolecular interactions. While intramolecular force field parameters can be determined by quantum mechanics, the parameterization of the intermolecular part is often tedious. Recently, an empirical procedure, based on the minimization of a loss function between simulated and experimental physical properties, was published by the authors. Thereby, efficient gradient-based numerical optimization algorithms were used. However, empirical force field optimization is inhibited by the two following central issues appearing in molecular simulations: firstly, they are extremely time-consuming, even on modern and high-performance computer clusters, and secondly, simulation data is affected by statistical noise. The latter provokes the fact that an accurate computation of gradients or Hessians is nearly impossible close to a local or global minimum, mainly because the loss function is flat. Therefore, the question arises of whether to apply a derivative-free method approximating the loss function by an appropriate model function. In this paper, a new Sparse Grid-based Optimization Workflow (SpaGrOW is presented, which accomplishes this task robustly and, at the same time, keeps the number of time-consuming simulations relatively small. This is achieved by an efficient sampling procedure

  8. Topologies, structures and parameter files for lipid simulations in GROMACS with the OPLS-aa force field: DPPC, POPC, DOPC, PEPC, and cholesterol

    Directory of Open Access Journals (Sweden)

    Waldemar Kulig

    2015-12-01

    Full Text Available In this data article we provide topologies and force field parameters files for molecular dynamics simulations of lipids in the OPLS-aa force field using the GROMACS package. This is the first systematic parameterization of lipid molecules in this force field. Topologies are provided for four phosphatidylcholines: saturated DPPC, mono-cis unsaturated POPC and DOPC, and mono-trans unsaturated PEPC. Parameterization of the phosphatidylcholines was achieved in two steps: first, we supplemented the OPLS force field parameters for DPPC with new parameters for torsion angles and van der Waals parameters for the carbon and hydrogen atoms in the acyl chains, as well as new partial atomic charges and parameters for torsion angles in the phosphatidylcholine and glycerol moieties [1]. Next, we derived parameters for the cis and trans double bonds and the neighboring them single bonds [2]. Additionally, we provide GROMACS input files with parameters describing simulation conditions (md.mdp, which are strongly recommended to be used with these lipids models. The data are associated with the research article “Cis and trans unsaturated phosphatidylcholine bilayers: a molecular dynamics simulation study” [2] and provided as supporting materials.

  9. Revisiting the droplet simulation approach to derive force-field parameters for water on molybdenum disulfide from wetting angle measurements

    Science.gov (United States)

    Leroy, Frédéric

    2016-10-01

    Owing to its peculiar electronic properties, molybdenum disulfide (MoS2) has been the subject of a growing number of studies in the recent years. In applications, this material and other transition metal dichalcogenides (TMDs) may have to interact with a liquid or polymer phase as well as solutions of biomolecules. It is therefore of primary importance to understand the wetting and adhesion properties of TMDs. Starting from existing models, we derive Lennard-Jones parameters for the interaction between water and the basal plane of MoS2 that are consistent with recent wetting experiments. Molecular dynamics simulations indicate that a stack of only two MoS2 monolayers is necessary to capture the wetting behavior of bulk MoS2. It is found that the Coulomb interaction between water and monolayer and bilayer MoS2 plays no role in the related interfacial thermodynamics. Calculations with the optimized parameters show that the depth of the well of the interaction potential between water and bulk MoS2 is of the order of 8.2 kJ/mol. Such a value is comparable with what was found for graphite and consistent with the fact that the wetting angles of water on graphite and MoS2 are almost equal. The derivation of the force-field parameters is performed using a methodology which, contrary to previous studies, makes a consistent use of droplet calculations. The results of our work should find application in further simulation studies on the wetting behavior of TMDs and other dispersive materials.

  10. Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

    Science.gov (United States)

    Bandura, A V; Sofo, J O; Kubicki, J D

    2006-04-27

    Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

  11. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue.

    Science.gov (United States)

    Wise, Olivia; Coskuner, Orkid

    2014-06-30

    Transition metal ion complexation with proteins is ubiquitous across such diverse fields as neurodegenerative and cardiovascular diseases and cancer. In this study, the structures of divalent copper ion centers including three histidine and one oxygen-ligated amino acid residues and the relative binding affinities of the oxygen-ligated amino acid residues with these metal ion centers, which are debated in the literature, are presented. Furthermore, new force field parameters, which are currently lacking for the full-length metal-ligand moieties, are developed for metalloproteins that have these centers. These new force field parameters enable investigations of metalloproteins possessing these binding sites using molecular simulations. In addition, the impact of using the atom equivalence and inequivalence atomic partial charge calculation procedures on the simulated structures of these metallopeptides, including hydration properties, is described.

  12. Accounting for electronic polarization in non-polarizable force fields

    Science.gov (United States)

    Leontyev, Igor; Stuchebrukhov, Alexei

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole $\\mu$~3D reported in recent ab initio and experimental studies with the value $\\mu_{eff}$~2.3D typically used in the empirical potentials, such as TIP3P or SPC/E. It is shown that the effective dipole of water can be understood as a scaled value $\\mu_{eff}=\\mu/\\sqrt{\\epsilon_{el}}$, where $\\epsilon_{el}$=1.78 is the electronic (high-frequency) dielectric constant of water. This simple theoretical framework provides important insights into the nature of the effective parameters, which is crucial when the computational models of liquid water are used for simulations in different environments, such as proteins, or for interaction with solutes.

  13. Modification of 56ACARBO force field for molecular dynamic calculations of chitosan and its derivatives.

    Science.gov (United States)

    Naumov, Vladimir S; Ignatov, Stanislav K

    2017-08-01

    The GROMOS 56ACARBO force field for the description of carbohydrates was modified for calculations of chitosan (poly-1,4-(N-acetyl)-β-D-glucopyranosamine-2) with protonated and non-protonated amino groups and its derivatives. Additional parameterization was developed on the basis of quantum chemical calculations. The modified force field (56ACARBO_CHT) allows performing the molecular dynamic calculations of chitosans with different degrees of protonation corresponding to various acidity of medium. Test calculations of the conformational transitions in the chitosan rings and polymeric chains as well as the chitosan nanocrystal dissolution demonstrate good agreement with experimental data. Graphical abstract The GROMOS 56ACARBO_CHT force field allows performing the molecular dynamic calculations of chitosans with different types of amio-group: free, protonated, substituted.

  14. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

    Science.gov (United States)

    Baker, Christopher M; Lopes, Pedro E M; Zhu, Xiao; Roux, Benoît; Mackerell, Alexander D

    2010-03-01

    Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule.

  15. Interaction of charged amino-acid side chains with ions: an optimization strategy for classical force fields.

    Science.gov (United States)

    Kahlen, Jens; Salimi, Leila; Sulpizi, Marialore; Peter, Christine; Donadio, Davide

    2014-04-10

    Many well-established classical biomolecular force fields, fitted on the solvation properties of single ions, do not necessarily describe all the details of ion pairing accurately, especially for complex polyatomic ions. Depending on the target application, it might not be sufficient to reproduce the thermodynamics of ion pairing, but it may also be necessary to correctly capture structural details, such as the coordination mode. In this work, we analyzed how classical force fields can be optimized to yield a realistic description of these different aspects of ion pairing. Given the prominent role of the interactions of negatively charged amino-acid side chains and divalent cations in many biomolecular systems, we chose calcium acetate as a benchmark system to devise a general optimization strategy that we applied to two popular force fields, namely, GROMOS and OPLS-AA. Using experimental association constants and first-principles molecular dynamics simulations as a reference, we found that small modifications of the van der Waals ion-ion interaction parameters allow a systematic improvement of the essential thermodynamic and structural properties of ion pairing.

  16. Polarizable force fields.

    Science.gov (United States)

    Antila, Hanne S; Salonen, Emppu

    2013-01-01

    This chapter provides an overview of the most common methods for including an explicit description of electronic polarization in molecular mechanics force fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.

  17. Polarizable Simulations with Second order Interaction Model – force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations

    Science.gov (United States)

    Kaminski, George A.; Ponomarev, Sergei Y.; Liu, Aibing B.

    2009-01-01

    We are presenting POSSIM (POlarizable Simulations with Second order Interaction Model) – a software package and a set of parameters designed for molecular simulations. The key feature of POSSIM is that the electrostatic polarization is taken into account using a previously introduced fast formalism. This permits cutting computational cost of using the explicit polarization by about an order of magnitude. In this article, parameters for water, methane, ethane, propane, butane, methanol and NMA are introduced. These molecules are viewed as model systems for protein simulations. We have achieved our goal of ca. 0.5 kcal/mol accuracy for gas-phase dimerization energies and no more than 2% deviations in liquid state heats of vaporization and densities. Moreover, free energies of hydration of the polarizable methane, ethane and methanol have been calculated using the statistical perturbation theory. These calculations are a model for calculating protein pKa shifts and ligand binding affinities. The free energies of hydration were found to be 2.12 kcal/mol, 1.80 kcal/mol and −4.95 kcal/mol for methane, ethane and methanol, respectively. The experimentally determined literature values are 1.91 kcal/mol, 1.83 kcal/mol and −5.11 kcal/mol. The POSSIM average error in these absolute free energies of hydration is only about 0.13 kcal/mol. Using the statistical perturbation theory with polarizable force fields is not widespread, and we believe that this work opens road to further development of the POSSIM force field and its applications for obtaining accurate energies in protein-related computer modeling. PMID:20209038

  18. Development of Site-Specific Mg(2+)-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations.

    Science.gov (United States)

    Casalino, Lorenzo; Palermo, Giulia; Abdurakhmonova, Nodira; Rothlisberger, Ursula; Magistrato, Alessandra

    2017-01-10

    The vital contribution of Mg(2+) ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg(2+) exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg(2+) force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg(2+) ions in different coordination motifs. As a result, a total of ∼2.5 μs MD simulations (100/200 ns for each run) for two prototypical Mg(2+)-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg(2+)-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg(2+) ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg(2+) ion parameters is not in line with the physical origin of the Mg(2+)-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg(2+) models and provides novel insights for the rational development of next-generation Mg(2+) FFs to be employed for atomistic simulations of RNA.

  19. Secondary Structure of Rat and Human Amylin across Force Fields.

    Directory of Open Access Journals (Sweden)

    Kyle Quynn Hoffmann

    Full Text Available The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient

  20. Derivation of Force field Parameters for SnO2-H2O Surface Systems from Plane-Wave Density Functional Theory Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wesolowski, David J [ORNL; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Sofo, Jorge O. [Pennsylvania State University; Kubicki, James D. [Pennsylvania State University

    2006-01-01

    Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO{sub 2} (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H{sub 2}O present. A classical interatomic force field has been developed to describe bulk SnO{sub 2} and SnO{sub 2}-H{sub 2}O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO{sub 2} are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H{sub 2}O molecules agree well between the ab initio and force field predictions. H{sub 2}O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

  1. Accounting for electronic polarization in nonpolarizable force fields

    CERN Document Server

    Leontyev, Igor

    2015-01-01

    The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER, GROMOS, etc should be scaled by a factor about 0.7. Our model explains why a neglect of electronic solvation energy, which typically amounts to about a half of total solvation energy, in non-polarizable simulations with un-scaled charges can produce a correct result; however, the correct solvation energy of ions does not guarantee the correctness of ion-ion pair interactions in many non-polarizable simulations. The inclusion of electronic screening for charged moieties is shown to result in significant changes in protein dynamics and can give rise to new qualitative results compared with the traditional non-polarizable force field simulations. The model also explains the striking difference between the value of water dipole $\\mu$~3D reported in recent ab initio and experimental s...

  2. Approximate photochemical dynamics of azobenzene with reactive force fields

    Science.gov (United States)

    Li, Yan; Hartke, Bernd

    2013-12-01

    We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work).

  3. Approximate photochemical dynamics of azobenzene with reactive force fields.

    Science.gov (United States)

    Li, Yan; Hartke, Bernd

    2013-12-14

    We have fitted reactive force fields of the ReaxFF type to the ground and first excited electronic states of azobenzene, using global parameter optimization by genetic algorithms. Upon coupling with a simple energy-gap transition probability model, this setup allows for completely force-field-based simulations of photochemical cis→trans- and trans→cis-isomerizations of azobenzene, with qualitatively acceptable quantum yields. This paves the way towards large-scale dynamics simulations of molecular machines, including bond breaking and formation (via the reactive force field) as well as photochemical engines (presented in this work).

  4. MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

    Science.gov (United States)

    Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

  5. Optimized molecular force field for sulfur hexafluoride simulations.

    Science.gov (United States)

    Olivet, Aurelio; Vega, Lourdes F

    2007-04-14

    An optimized molecular force field for sulfur hexafluoride (SF6) simulations is presented in this work. The new force field for SF6 contains two parts: a Lennard-Jones potential that deals with F-F intermolecular interactions and the second term dealing with the intramolecular forces. In this second part the flexibility of the molecule is explicitly considered by 6 harmonic stretch terms, modeling the S-F chemical bonds, and 12 harmonic bending terms, modeling the F-S-F angular deformations. The parameters of the new force field have been obtained by a multivariable optimization procedure, whose main feature is the simultaneous fitting of all force field parameters, using as reference data several equilibrium properties (vapor pressure, saturated liquid density, and surface tension) and shear viscosity. The new force field clearly improves the description of the phase envelope and the rest of the properties as compared to previous simulations for a rigid model for the same molecule [A. Olivet et al., J. Chem. Phys. 123, 194508 (2005)]. Results for the optimized force field concerning the vapor-liquid coexistence curve, several thermodynamics states at the homogeneous gas and liquid region, and transport coefficients of SF6 are in good agreement with available experimental data.

  6. Application of the multi-parameter SQM harmonic force field, and ESFF harmonic frequencies scaling procedures to the determination of the vibrational spectra of silicon- and sulfur(II)-containing compounds.

    Science.gov (United States)

    Borowski, Piotr; Ruiz, Tomas Peña; Barczak, Mariusz; Pilorz, Karol; Pasieczna-Patkowska, Sylwia

    2012-02-01

    Multi-parameter scaling techniques, such as Scaled Quantum Mechanical (SQM) force field [J. Am. Chem. Soc. 105 (1983) 7037-7047; J. Phys. Chem. A 102 (1998) 1412-1424] or Effective Scaling Frequency Factor (ESFF) [Chem. Phys. Lett. 446 (2007) 191-198; J. Mol. Spectrosc. 264 (2010) 66-74] techniques, are very powerful in the theoretical prediction of the vibrational spectra of complex molecules. In the present work sets of transferable SQM and ESFF scaling factors (within the valence coordinates based schemes) that can be applied to silicon- and sulfur(II)-containing compounds have been determined. A number of VDZ- and VTZ-quality basis sets were used in conjunction with the B3LYP density functional. Eight molecules typically used in the synthesis of silica-based materials were chosen, and theoretical modes were assigned to bands detected on their IR or Raman spectra. This set was augmented with a set of 10 auxiliary, sulfur(II)-containing molecules, for which only "pure" vibrations involving S-containing motifs were assigned. This led to the set of more than 600 individual vibrations. Five factors attributed to these motifs were optimized. Scaling factors attributed to the characteristic types of internal coordinates including the second-row atoms and chlorine, which are applicable to the present molecules were preset. Their values, optimized for Baker's training set of molecules [J. Phys. Chem. A 102 (1998) 1412-1424] for all basis sets considered in this work, were also found, extending thus the applicability of the multi-parameter scaling methods. New scaling factors exhibit low statistical uncertainties. Reasonable agreement between experimental and SQM- or ESFF-scaled frequencies was obtained even for the 6-31G* basis set (RMSSQM scaling factors were found to occasionally exhibit large deviations from unity, which is to be contrasted with ESFF scaling factors.

  7. Intercomparison of stratospheric ozone profiles for the assessment of the upgraded GROMOS radiometer at Bern

    Directory of Open Access Journals (Sweden)

    S. Studer

    2013-07-01

    Full Text Available Since November 1994, the GROund-based Millimeter-wave Ozone Spectrometer (GROMOS measures stratospheric and lower mesospheric ozone in Bern, Switzerland (47.95° N, 7.44° E. GROMOS is part of the Network for the Detection of Atmospheric Composition Change (NDACC. In July 2009, a Fast-Fourier-Transform spectrometer (FFTS has been added as backend to GROMOS. The new FFTS and the original filter bench (FB measured parallel for over two years. In October 2011, the FB has been turned off and the FFTS is now used to continue the ozone time series. For a consolidated ozone time series in the frame of NDACC, the quality of the stratospheric ozone profiles obtained with the FFTS has to be assessed. The FFTS results from July 2009 to December 2011 are compared to ozone profiles retrieved by the FB. FFTS and FB of the GROMOS microwave radiometer agree within 5% above 20 hPa. A later harmonization of both time series will be realized by taking the FFTS as benchmark for the FB. Ozone profiles from the FFTS are also compared to coinciding lidar measurements from the Observatoire Haute Provence (OHP, France. For the time period studied a maximum mean difference (lidar – GROMOS FFTS of +3.8% at 3.1 hPa and a minimum mean difference of +1.4% at 8 hPa is found. Further, intercomparisons with ozone profiles from other independent instruments are performed: satellite measurements include MIPAS onboard ENVISAT, SABER onboard TIMED, MLS onboard EOS Aura and ACE-FTS onboard SCISAT-1. Additionally, ozonesondes launched from Payerne, Switzerland, are used in the lower stratosphere. Mean relative differences of GROMOS FFTS and these independent instruments are less than 10% between 50 and 0.1 hPa.

  8. Effects of Different Force Fields and Temperatures on the Structural Character of Abeta (12–28 Peptide in Aqueous Solution

    Directory of Open Access Journals (Sweden)

    Jihua Wang

    2011-11-01

    Full Text Available The aim of this work is to investigate the effects of different force fields and temperatures on the structural character of Aβ (12–28 peptide in aqueous solution. Moreover, the structural character of Aβ (12–28 peptide is compared with other amyloid peptides (such as H1 and α-syn12 peptide. The two independent temperature replica exchange molecular dynamics (T-REMD simulations were completed by using two different models (OPLS-AA/TIP4P and GROMOS 43A1/SPC. We compared the models by analyzing the distributions of backbone dihedral angles, the secondary structure propensity, the free energy surface and the formation of β-hairpin. The results show that the mostly populated conformation state is random coil for both models. The population of β-hairpin is below 8 percent for both models. However, the peptide modeled by GROMOS 43A1 form β-hairpin with turn located at residues F19-E22, while the peptide modeled by OPLS-AA form β-hairpin with turn located at residues L17-F20.

  9. Parallelization of the molecular dynamics code GROMOS87 for distributed memory parallel architectures

    NARCIS (Netherlands)

    Green, DG; Meacham, KE; vanHoesel, F; Hertzberger, B; Serazzi, G

    1995-01-01

    This paper describes the techniques and methodologies employed during parallelization of the Molecular Dynamics (MD) code GROMOS87, with the specific requirement that the program run efficiently on a range of distributed-memory parallel platforms. We discuss the preliminary results of our parallel

  10. Tailor-made force fields for crystal-structure prediction.

    Science.gov (United States)

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

  11. Transition States from Empirical Force Fields

    DEFF Research Database (Denmark)

    Jensen, Frank; Norrby, Per-Ola

    2003-01-01

    This is an overview of the use of empirical force fields in the study of reaction mechanisms. EVB-type methods (including RFF and MCMM) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate...

  12. Polarization effects in molecular mechanical force fields

    Science.gov (United States)

    Cieplak, Piotr; Dupradeau, François-Yves; Duan, Yong; Wang, Junmei

    2014-01-01

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component—polarization energy—and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. PMID:21828594

  13. Polarization effects in molecular mechanical force fields

    Energy Technology Data Exchange (ETDEWEB)

    Cieplak, Piotr [Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92120 (United States); Dupradeau, Francois-Yves [UMR CNRS 6219-Faculte de Pharmacie, Universite de Picardie Jules Verne, 1 rue des Louvels, F-80037 Amiens (France); Duan, Yong [Genome Center and Department of Applied Science, University of California, Davis, One Shields Avenue, Davis, CA 95616 (United States); Wang Junmei, E-mail: pcieplak@burnham.or [Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Boulevard, ND9.136, Dallas, TX 75390-9050 (United States)

    2009-08-19

    The focus here is on incorporating electronic polarization into classical molecular mechanical force fields used for macromolecular simulations. First, we briefly examine currently used molecular mechanical force fields and the current status of intermolecular forces as viewed by quantum mechanical approaches. Next, we demonstrate how some components of quantum mechanical energy are effectively incorporated into classical molecular mechanical force fields. Finally, we assess the modeling methods of one such energy component-polarization energy-and present an overview of polarizable force fields and their current applications. Incorporating polarization effects into current force fields paves the way to developing potentially more accurate, though more complex, parameterizations that can be used for more realistic molecular simulations. (topical review)

  14. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters

    DEFF Research Database (Denmark)

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia

    2016-01-01

    In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present ...... (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3]....

  15. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  16. Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

    OpenAIRE

    Savelyev, Alexey; MacKerell, Alexander D.

    2014-01-01

    Recently we presented a first-generation all-atom Drude polarizable force field for DNA based on the classical Drude oscillator model, focusing on optimization of key dihedral angles followed by extensive validation of the force field parameters. Presently, we describe the procedure for balancing the electrostatic interactions between ions, water, and DNA as required for development of the Drude force field for DNA. The proper balance of these interactions is shown to impact DNA stability and...

  17. Consistent force fields for saccharides

    DEFF Research Database (Denmark)

    Rasmussen, Kjeld

    1999-01-01

    atoms. Charges are modeled such that Mulliken population analyses are reproduced. Morse functions are used for all bonded interactions; experimentally deriveddissociation energies are used as parameters. Van der Waals interactions are modeled with Lennard-Jones 12-6 functions.The anomeric and exo...

  18. The Dependence of Amyloid‐β Dynamics on Protein Force Fields and Water Models

    DEFF Research Database (Denmark)

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2015-01-01

    We studied the dynamics of Aβ40, involved in Alzheimer's disease, by using 21 methods combined from Amber03, Amber99sb‐ILDN, Charmm27, Charmm22*, OPLS‐2001, OPLS‐2006, OPLS‐2008, Gromos96‐43a1, Gromos96‐53a6, Gromos96‐54a7, and the water models SPC, TIP3P, TIP4P. Major differences in the structural...

  19. Using J-coupling constants for force field validation: application to hepta-alanine.

    Science.gov (United States)

    Georgoulia, Panagiota S; Glykos, Nicholas M

    2011-12-29

    A computational solution to the protein folding problem is the holy grail of biomolecular simulation and of the corresponding force fields. The complexity of the systems used for folding simulations precludes a direct feedback between the simulations and the force fields, thus necessitating the study of simpler systems with sufficient experimental data to allow force field optimization and validation. Recent studies on short polyalanine peptides of increasing length (up to penta-alanine) indicated the presence of a systematic deviation between the experimental (NMR-derived) J-couplings and the great majority of biomolecular force fields, with the χ(2) values for even the best-performing force fields being in the 1.4-1.8 range. Here we show that by increasing the number of residues to seven and by achieving convergence through an increase of the simulation time to 2 μs, we can identify one force field (the AMBER99SB force field, out of the three force fields studied) which when compared with the experimental J-coupling data (and for a specific set of Karplus equation parameters and estimated J-coupling errors previously used in the literature) gave a value of χ(2) = 0.99, indicating that full statistical consistency between experiment and simulation is feasible. However, and as a detailed analysis of the effects of estimated errors shows, the χ(2) values may be unsuitable as indicators of the goodness of fit of the various biomolecular force fields. © 2011 American Chemical Society

  20. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

    Science.gov (United States)

    Rzepiela, Andrzej J; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J

    2011-06-14

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1:1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein

  1. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  2. Systematic Parameterization of Lignin for the CHARMM Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Vermaas, Joshua; Petridis, Loukas; Beckham, Gregg; Crowley, Michael

    2017-07-06

    Plant cell walls have three primary components, cellulose, hemicellulose, and lignin, the latter of which is a recalcitrant, aromatic heteropolymer that provides structure to plants, water and nutrient transport through plant tissues, and a highly effective defense against pathogens. Overcoming the recalcitrance of lignin is key to effective biomass deconstruction, which would in turn enable the use of biomass as a feedstock for industrial processes. Our understanding of lignin structure in the plant cell wall is hampered by the limitations of the available lignin forcefields, which currently only account for a single linkage between lignins and lack explicit parameterization for emerging lignin structures both from natural variants and engineered lignin structures. Since polymerization of lignin occurs via radical intermediates, multiple C-O and C-C linkages have been isolated , and the current force field only represents a small subset of lignin the diverse lignin structures found in plants. In order to take into account the wide range of lignin polymerization chemistries, monomers and dimer combinations of C-, H-, G-, and S-lignins as well as with hydroxycinnamic acid linkages were subjected to extensive quantum mechanical calculations to establish target data from which to build a complete molecular mechanics force field tuned specifically for diverse lignins. This was carried out in a GPU-accelerated global optimization process, whereby all molecules were parameterized simultaneously using the same internal parameter set. By parameterizing lignin specifically, we are able to more accurately represent the interactions and conformations of lignin monomers and dimers relative to a general force field. This new force field will enables computational researchers to study the effects of different linkages on the structure of lignin, as well as construct more accurate plant cell wall models based on observed statistical distributions of lignin that differ between

  3. First Principles Force Field for Metallic Tantalum

    OpenAIRE

    Strachan, Alejandro; Cagin, Tahir; Gulseren, Oguz; Mukherjee, Sonali; Cohen, Ronald E.; Goddard III, William A.

    2002-01-01

    We propose a general strategy to develop accurate Force Fields (FF) for metallic systems derived from ab initio quantum mechanical (QM) calculations; we illustrate this approach for tantalum. As input data to the FF we use the linearized augmented plane wave method (LAPW) with the generalized gradient approximation (GGA) to calculate: (i) the zero temperature equation of state (EOS) of Ta for bcc, fcc, and hcp crystal structures for pressures up to ~500 GPa. (ii) Elastic constants. (iii) We u...

  4. A test on reactive force fields for the study of silica dimerization reactions

    Energy Technology Data Exchange (ETDEWEB)

    Moqadam, Mahmoud; Riccardi, Enrico; Trinh, Thuat T.; Åstrand, Per-Olof; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117, 7491 Trondheim (Norway)

    2015-11-14

    We studied silica dimerization reactions in the gas and aqueous phase by density functional theory (DFT) and reactive force fields based on two parameterizations of ReaxFF. For each method (both ReaxFF force fields and DFT), we performed constrained geometry optimizations, which were subsequently evaluated in single point energy calculations using the other two methods. Standard fitting procedures typically compare the force field energies and geometries with those from quantum mechanical data after a geometry optimization. The initial configurations for the force field optimization are usually the minimum energy structures of the ab initio database. Hence, the ab initio method dictates which structures are being examined and force field parameters are being adjusted in order to minimize the differences with the ab initio data. As a result, this approach will not exclude the possibility that the force field predicts stable geometries or low transition states which are realistically very high in energy and, therefore, never considered by the ab initio method. Our analysis reveals the existence of such unphysical geometries even at unreactive conditions where the distance between the reactants is large. To test the effect of these discrepancies, we launched molecular dynamics simulations using DFT and ReaxFF and observed spurious reactions for both ReaxFF force fields. Our results suggest that the standard procedures for parameter fitting need to be improved by a mutual comparative method.

  5. Hierarchical atom type definitions and extensible all-atom force fields.

    Science.gov (United States)

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc.

  6. Force field dependence of riboswitch dynamics.

    Science.gov (United States)

    Hanke, Christian A; Gohlke, Holger

    2015-01-01

    Riboswitches are noncoding regulatory elements that control gene expression in response to the presence of metabolites, which bind to the aptamer domain. Metabolite binding appears to occur through a combination of conformational selection and induced fit mechanism. This demands to characterize the structural dynamics of the apo state of aptamer domains. In principle, molecular dynamics (MD) simulations can give insights at the atomistic level into the dynamics of the aptamer domain. However, it is unclear to what extent contemporary force fields can bias such insights. Here, we show that the Amber force field ff99 yields the best agreement with detailed experimental observations on differences in the structural dynamics of wild type and mutant aptamer domains of the guanine-sensing riboswitch (Gsw), including a pronounced influence of Mg2+. In contrast, applying ff99 with parmbsc0 and parmχOL modifications (denoted ff10) results in strongly damped motions and overly stable tertiary loop-loop interactions. These results are based on 58 MD simulations with an aggregate simulation time>11 μs, careful modeling of Mg2+ ions, and thorough statistical testing. Our results suggest that the moderate stabilization of the χ-anti region in ff10 can have an unwanted damping effect on functionally relevant structural dynamics of marginally stable RNA systems. This suggestion is supported by crystal structure analyses of Gsw aptamer domains that reveal χ torsions with high-anti values in the most mobile regions. We expect that future RNA force field development will benefit from considering marginally stable RNA systems and optimization toward good representations of dynamics in addition to structural characteristics.

  7. MATCH: an atom-typing toolset for molecular mechanics force fields.

    Science.gov (United States)

    Yesselman, Joseph D; Price, Daniel J; Knight, Jennifer L; Brooks, Charles L

    2012-01-15

    We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized.

  8. Dissolution study of active pharmaceutical ingredients using molecular dynamics simulations with classical force fields

    Science.gov (United States)

    Greiner, Maximilian; Elts, Ekaterina; Schneider, Julian; Reuter, Karsten; Briesen, Heiko

    2014-11-01

    The CHARMM, general Amber and OPLS force fields are evaluated for their suitability in simulating the molecular dynamics of the dissolution of the hydrophobic, small-molecule active pharmaceutical ingredients aspirin, ibuprofen, and paracetamol in aqueous media. The force fields are evaluated by comparison with quantum chemical simulations or experimental references on the basis of the following capabilities: accurately representing intra- and intermolecular interactions, appropriately reproducing crystal lattice parameters, adequately describing thermodynamic properties, and the qualitative description of the dissolution behavior. To make this approach easily accessible for evaluating the dissolution properties of novel drug candidates in the early stage of drug development, the force field parameter files are generated using online resources such as the SWISS PARAM servers, and the software packages ACPYPE and Maestro. All force fields are found to reproduce the intermolecular interactions with a reasonable degree of accuracy, with the general Amber and CHARMM force fields showing the best agreement with quantum mechanical calculations. A stable crystal bulk structure is obtained for all model substances, except for ibuprofen, where the reproductions of the lattice parameters and observed crystal stability are considerably poor for all force fields. The heat of solution used to evaluate the solid-to-solution phase transitions is found to be in qualitative agreement with the experimental data for all combinations tested, with the results being quantitatively optimum for the general Amber and CHARMM force fields. For aspirin and paracetamol, stable crystal-water interfaces were obtained. The (100), (110), (011) and (001) interfaces of aspirin or paracetamol and water were simulated for each force field for 30 ns. Although generally expected as a rare event, in some of the simulations, dissolution is observed at 310 K and ambient pressure conditions.

  9. Direct reaction field force field : A consistent way to connect and combine quantum-chemical and classical descriptions of molecules

    NARCIS (Netherlands)

    VanDuijnen, PT; DeVries, AH

    1996-01-01

    The direct reaction field (DRF) force field gives a classical description of intermolecular interactions based on ab initio quantum-chemical descriptions of matter. The parameters of the DRF force field model molecular electrostatic and response properties, which are represented by distributed charg

  10. Parameterization and optimization of the menthol force field for molecular dynamics simulations.

    Science.gov (United States)

    Jasik, Mateusz; Szefczyk, Borys

    2016-10-01

    Menthol's various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.

  11. Management of change through force field analysis.

    Science.gov (United States)

    Baulcomb, Jean Sandra

    2003-07-01

    Today's NHS is rapidly changing, placing more emphasis on the managerial responsibilities of ward managers. Managing change is seen as being skilled at creating, acquiring and transferring knowledge to reflect new knowledge and insights. Defining core concepts is often difficult and requires the drawing on models/theories of change for guidance. Guidance from Lewin's (1951) force field analysis demonstrates the complexities of the change process and how driving and resisting forces were incorporated within the planning and implementation phases. Findings outline the benefits of a small scale change for staff, patients and the organization when successfully used to introduce a change of shift pattern within a progressively busy haematology day unit, in order to meet service demands without additional funding. Conclusions have been drawn in relation to the process and recommendations for practice made to further enhance care delivery within the unit.

  12. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics.

    Science.gov (United States)

    Yin, Jian; Fenley, Andrew T; Henriksen, Niel M; Gilson, Michael K

    2015-08-13

    Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by nonoptimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery.

  13. Reactive Force Fields via Explicit Valency

    Science.gov (United States)

    Kale, Seyit

    Computational simulations are invaluable in elucidating the dynamics of biological macromolecules. Unfortunately, reactions present a fundamental challenge. Calculations based on quantum mechanics can predict bond formation and rupture; however they suffer from severe length- and time-limitations. At the other extreme, classical approaches provide orders of magnitude faster simulations; however they regard chemical bonds as immutable entities. A few exceptions exist, but these are not always trivial to adopt for routine use. We bridge this gap by providing a novel, pseudo-classical approach, based on explicit valency. We unpack molecules into valence electron pairs and atomic cores. Particles bear ionic charges and interact via pairwise-only potentials. The potentials are informed of quantum effects in the short-range and obey dissociation limits in the long-range. They are trained against a small set of isolated species, including geometries and thermodynamics of small hydrides and of dimers formed by them. The resulting force field captures the essentials of reactivity, polarizability and flexibility in a simple, seamless setting. We call this model LEWIS, after the chemical theory that inspired the use of valence pairs. Following the introduction in Chapter 1, we initially focus on the properties of water. Chapter 2 considers gas phase clusters. To transition to the liquid phase, Chapter 3 describes a novel pairwise long-range compensation that performs comparably to infinite lattice summations. The approach is suited to ionic solutions in general. In Chapters 4 and 5, LEWIS is shown to correctly predict the dipolar and quadrupolar response in bulk liquid, and can accommodate proton transfers in both acid and base. Efficiency permits the study of proton defects at dilutions not accessible to experiment or quantum mechanics. Chapter 6 discusses explicit valency approaches in other hydrides, forming the basis of a reactive organic force field. Examples of simple

  14. Atomic Radii in Molecules for Use in a Polarizable Force Field

    NARCIS (Netherlands)

    Swart, Marcel; Van Duijnen, Piet Th

    2011-01-01

    We report here the results for an ab initio approach to obtain the parameters needed for molecular simulations using a polarizable force field. These parameters consist of the atomic charges, polarizabilities, and radii. The former two are readily obtained using methods reported previously (van Duij

  15. POSSIM: Parameterizing Complete Second-Order Polarizable Force Field for Proteins.

    Science.gov (United States)

    Li, Xinbi; Ponomarev, Sergei Y; Sigalovsky, Daniel L; Cvitkovic, John P; Kaminski, George A

    2014-11-11

    Previously, we reported development of a fast polarizable force field and software named POSSIM (POlarizable Simulations with Second order Interaction Model). The second-order approximation permits the speed up of the polarizable component of the calculations by ca. an order of magnitude. We have now expanded the POSSIM framework to include a complete polarizable force field for proteins. Most of the parameter fitting was done to high-level quantum mechanical data. Conformational geometries and energies for dipeptides have been reproduced within average errors of ca. 0.5 kcal/mol for energies of the conformers (for the electrostatically neutral residues) and 9.7° for key dihedral angles. We have also validated this force field by running Monte Carlo simulations of collagen-like proteins in water. The resulting geometries were within 0.94 Å root-mean-square deviation (RMSD) from the experimental data. We have performed additional validation by studying conformational properties of three oligopeptides relevant in the context of N-glycoprotein secondary structure. These systems have been previously studied with combined experimental and computational methods, and both POSSIM and benchmark OPLS-AA simulations that we carried out produced geometries within ca. 0.9 Å RMSD of the literature structures. Thus, the performance of POSSIM in reproducing the structures is comparable with that of the widely used OPLS-AA force field. Furthermore, our fitting of the force field parameters for peptides and proteins has been streamlined compared with the previous generation of the complete polarizable force field and relied more on transferability of parameters for nonbonded interactions (including the electrostatic component). The resulting deviations from the quantum mechanical data are similar to those achieved with the previous generation; thus, the technique is robust, and the parameters are transferable. At the same time, the number of parameters used in this work was

  16. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

    Science.gov (United States)

    Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

    2017-06-05

    Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Methodology of Parameterization of Molecular Mechanics Force Field From Quantum Chemistry Calculations using Genetic Algorithm: A case study of methanol

    CERN Document Server

    Li, Ying; Chan, Maria K Y; Sankaranarayanan, Subramanian; Rouxb, Benoît

    2016-01-01

    In molecular dynamics (MD) simulation, force field determines the capability of an individual model in capturing physical and chemistry properties. The method for generating proper parameters of the force field form is the key component for computational research in chemistry, biochemistry, and condensed-phase physics. Our study showed that the feasibility to predict experimental condensed phase properties (i.e., density and heat of vaporization) of methanol through problem specific force field from only quantum chemistry information. To acquire the satisfying parameter sets of the force field, the genetic algorithm (GA) is the main optimization method. For electrostatic potential energy, we optimized both the electrostatic parameters of methanol using the GA method, which leads to low deviations of between the quantum mechanics (QM) calculations and the GA optimized parameters. We optimized the van der Waals (vdW) parameters both using GA and guided GA methods by calibrating interaction energy of various met...

  18. Parametrization of a Reactive Force Field (ReaxFF) for Molecular Dynamics Simulations of Si Nanoparticles.

    Science.gov (United States)

    Barcaro, Giovanni; Monti, Susanna; Sementa, Luca; Carravetta, Vincenzo

    2017-08-08

    A novel computational approach, based on classical reactive molecular dynamics simulations (RMD) and quantum chemistry (QC) global energy optimizations, is proposed for modeling large Si nanoparticles. The force field parameters, which can describe bond breaking and formation, are derived by reproducing energetic and structural properties of a set of Si clusters increasing in size. These reference models are obtained through a new protocol based on a joint high temperature RMD/low temperature Basin Hopping QC search. The different procedures of estimating optimal force field parameters and their performance are discussed in detail.

  19. Thermodynamic properties for applications in chemical industry via classical force fields.

    Science.gov (United States)

    Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran

    2012-01-01

    Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown.

  20. Force-field parameterization of the galactic cosmic ray spectrum: Validation for Forbush decreases

    Science.gov (United States)

    Usoskin, I. G.; Kovaltsov, G. A.; Adriani, O.; Barbarino, G. C.; Bazilevskaya, G. A.; Bellotti, R.; Boezio, M.; Bogomolov, E. A.; Bongi, M.; Bonvicini, V.; Bottai, S.; Bruno, A.; Cafagna, F.; Campana, D.; Carbone, R.; Carlson, P.; Casolino, M.; Castellini, G.; De Donato, C.; De Santis, C.; De Simone, N.; Di Felice, V.; Formato, V.; Galper, A. M.; Karelin, A. V.; Koldashov, S. V.; Koldobskiy, S.; Krutkov, S. Y.; Kvashnin, A. N.; Leonov, A.; Malakhov, V.; Marcelli, L.; Martucci, M.; Mayorov, A. G.; Menn, W.; Mergé, M.; Mikhailov, V. V.; Mocchiutti, E.; Monaco, A.; Mori, N.; Munini, R.; Osteria, G.; Palma, F.; Panico, B.; Papini, P.; Pearce, M.; Picozza, P.; Pizzolotto, C.; Ricci, M.; Ricciarini, S. B.; Rossetto, L.; Sarkar, R.; Scotti, V.; Simon, M.; Sparvoli, R.; Spillantini, P.; Stozhkov, Y. I.; Vacchi, A.; Vannuccini, E.; Vasilyev, G. I.; Voronov, S. A.; Yurkin, Y. T.; Zampa, G.; Zampa, N.; Zverev, V. G.

    2015-06-01

    A useful parametrization of the energy spectrum of galactic cosmic rays (GCR) near Earth is offered by the so-called force-field model which describes the shape of the entire spectrum with a single parameter, the modulation potential. While the usefulness of the force-field approximation has been confirmed for regular periods of solar modulation, it was not tested explicitly for disturbed periods, when GCR are locally modulated by strong interplanetary transients. Here we use direct measurements of protons and α -particles performed by the PAMELA space-borne instrument during December 2006, including a major Forbush decrease, in order to directly test the validity of the force-field parameterization. We conclude that (1) The force-field parametrization works very well in describing the energy spectra of protons and α -particles directly measured by PAMELA outside the Earths atmosphere; (2) The energy spectrum of GCR can be well parameterized by the force-field model also during a strong Forbush decrease; (3) The estimate of the GCR modulation parameter, obtained using data from the world-wide neutron monitor network, is in good agreement with the spectra directly measured by PAMELA during the studied interval. This result is obtained on the basis of a single event analysis, more events need to be analyzed.

  1. Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

    Science.gov (United States)

    Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M.

    2016-04-01

    Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures - while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

  2. The critical role of force-fields in property prediction

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Welsh, William J.; Rasmussen, Kjeld

    1999-01-01

    of conformational energydifferences and interaction energies vary significantly from one force-field to another. As a test for the reliability of the non-bonded interactions, vapor-liquid equilibrium (VLE) data have been calculated for a small number of systems using three different force-fields. The force...

  3. The harmonic force field and absolute infrared intensities of diacetylene

    NARCIS (Netherlands)

    Koops, Th.; Visser, T.; Smit, W.M.A.

    1984-01-01

    The frequencies, harmonic force field and absolute IR intensities for C4H2 and C4D2 are reported. The experimental harmonized frequencies obey the Teller—Redlich product rule very well. An approximate harmonic force field was obtained from a refinement procedure in which the starting values are adj

  4. First-Principles, Physically Motivated Force Field for the Ionic Liquid [BMIM][BF4].

    Science.gov (United States)

    Choi, Eunsong; McDaniel, Jesse G; Schmidt, J R; Yethiraj, Arun

    2014-08-07

    Molecular simulations play an important role in establishing structure-property relations in complex fluids such as room-temperature ionic liquids. Classical force fields are the starting point when large systems or long times are of interest. These force fields must be not only accurate but also transferable. In this work, we report a physically motivated force field for the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) based on symmetry-adapted perturbation theory. The predictions (from molecular dynamics simulations) of the liquid density, enthalpy of vaporization, diffusion coefficients, viscosity, and conductivity are in excellent agreement with experiment, with no adjustable parameters. The explicit energy decomposition inherent in the force field enables a quantitative analysis of the important physical interactions in these systems. We find that polarization is crucial and there is little evidence of charge transfer. We also argue that the often used procedure of scaling down charges in molecular simulations of ionic liquids is unphysical for [BMIM][BF4]. Because all intermolecular interactions in the force field are parametrized from first-principles, we anticipate good transferability to other ionic liquid systems and physical conditions.

  5. A first-principles based force-field for Li+ and OH- in ethanolic solution.

    Science.gov (United States)

    Milek, Theodor; Meyer, Bernd; Zahn, Dirk

    2013-10-14

    We report on the development of force-field parameters for accurately modeling lithium and hydroxide ions in ethanol in solution. Based on quantum calculations of small molecular clusters mimicking the solvent structure of individual ions as well as the solvated LiOH dimer, significant improvements of off-the-shelf force-fields are obtained. The quality of our model is demonstrated by comparison to ab initio molecular dynamics of the bulk solution and to experimental data available for ethanol/water mixtures.

  6. Fusing heterogeneous data for the calibration of molecular dynamics force fields using hierarchical Bayesian models.

    Science.gov (United States)

    Wu, Stephen; Angelikopoulos, Panagiotis; Tauriello, Gerardo; Papadimitriou, Costas; Koumoutsakos, Petros

    2016-12-28

    We propose a hierarchical Bayesian framework to systematically integrate heterogeneous data for the calibration of force fields in Molecular Dynamics (MD) simulations. Our approach enables the fusion of diverse experimental data sets of the physico-chemical properties of a system at different thermodynamic conditions. We demonstrate the value of this framework for the robust calibration of MD force-fields for water using experimental data of its diffusivity, radial distribution function, and density. In order to address the high computational cost associated with the hierarchical Bayesian models, we develop a novel surrogate model based on the empirical interpolation method. Further computational savings are achieved by implementing a highly parallel transitional Markov chain Monte Carlo technique. The present method bypasses possible subjective weightings of the experimental data in identifying MD force-field parameters.

  7. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    Science.gov (United States)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  8. reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

    Science.gov (United States)

    Müller, Julian; Hartke, Bernd

    2016-08-09

    Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

  9. A transferable force field to predict phase equilibria and surface tension of ethers and glycol ethers.

    Science.gov (United States)

    Ferrando, Nicolas; Lachet, Véronique; Pérez-Pellitero, Javier; Mackie, Allan D; Malfreyt, Patrice; Boutin, Anne

    2011-09-15

    We propose a new transferable force field to simulate phase equilibrium and interfacial properties of systems involving ethers and glycol ethers. On the basis of the anisotropic united-atom force field, only one new group is introduced: the ether oxygen atom. The optimized Lennard-Jones (LJ) parameters of this atom are identical whatever the molecule simulated (linear ether, branched ether, cyclic ether, aromatic ether, diether, or glycol ether). Accurate predictions are achieved for pure compound saturated properties, critical properties, and surface tensions of the liquid-vapor interface, as well as for pressure-composition binary mixture diagrams. Multifunctional molecules (1,2-dimethoxyethane, 2-methoxyethanol, diethylene glycol) have also been studied using a recently proposed methodology for the calculation of the intramolecular electrostatic energy avoiding the use of additional empirical parameters. This new force field appears transferable for a wide variety of molecules and properties. It is furthermore worth noticing that binary mixtures have been simulated without introducing empirical binary parameters, highlighting also the transferability to mixtures. Hence, this new force field gives future opportunities to simulate complex systems of industrial interest involving molecules with ether functions.

  10. Using force fields methods for locating transition structures

    Science.gov (United States)

    Jensen, Frank

    2003-11-01

    A previously proposed strategy of using force field methods for generating approximations to the geometry of transition structures is extended to also estimating an approximate Hessian matrix. These two components allow an automated method for locating first order saddle points, which is an essential requisite for studying chemical reactions of systems with many degrees of freedom. The efficiency of using an approximate force field Hessian matrix for initiating the geometry optimization is compared with the use of an exact Hessian. The force field Hessian in general requires more geometry steps to converge, but the additional computational cost is offset by the savings from not calculating the exact Hessian at the initial geometry.

  11. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing

    Science.gov (United States)

    Vanommeslaeghe, K.; MacKerell, A. D.

    2012-01-01

    Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF’s complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/. PMID:23146088

  12. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

    Science.gov (United States)

    Vanommeslaeghe, K; MacKerell, A D

    2012-12-21

    Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug-like molecules alone or interacting with biological systems. In simulations involving biological macromolecules, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and charges is required. In the present article, which is part I of a series of two, we present the algorithms for bond perception and atom typing for the CHARMM General Force Field (CGenFF). The CGenFF atom typer first associates attributes to the atoms and bonds in a molecule, such as valence, bond order, and ring membership among others. Of note are a number of features that are specifically required for CGenFF. This information is then used by the atom typing routine to assign CGenFF atom types based on a programmable decision tree. This allows for straightforward implementation of CGenFF's complicated atom typing rules and for equally straightforward updating of the atom typing scheme as the force field grows. The presented atom typer was validated by assigning correct atom types on 477 model compounds including in the training set as well as 126 test-set molecules that were constructed to specifically verify its different components. The program may be utilized via an online implementation at https://www.paramchem.org/ .

  13. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.

    Science.gov (United States)

    Harder, Edward; Damm, Wolfgang; Maple, Jon; Wu, Chuanjie; Reboul, Mark; Xiang, Jin Yu; Wang, Lingle; Lupyan, Dmitry; Dahlgren, Markus K; Knight, Jennifer L; Kaus, Joseph W; Cerutti, David S; Krilov, Goran; Jorgensen, William L; Abel, Robert; Friesner, Richard A

    2016-01-12

    The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.

  14. Transferable force field for carboxylate esters: application to fatty acid methylic ester phase equilibria prediction.

    Science.gov (United States)

    Ferrando, Nicolas; Lachet, Véronique; Boutin, Anne

    2012-03-15

    In this work, a new transferable united-atoms force field for carboxylate esters is proposed. All Lennard-Jones parameters are reused from previous parametrizations of the AUA4 force field, and only a unique set of partial electrostatic charges is introduced for the ester chemical function. Various short alkyl-chain esters (methyl acetate, ethyl acetate, methyl propionate, ethyl propionate) and two fatty acid methylic esters (methyl oleate and methyl palmitate) are studied. Using this new force field in Monte Carlo simulations, we show that various pure compound properties are accurately predicted: saturated liquid densities, vapor pressures, vaporization enthalpies, critical properties, liquid-vapor surface tensions. Furthermore, a good accuracy is also obtained in the prediction of binary mixture pressure-composition diagrams, without introducing empirical binary interaction parameters. This highlights the transferability of the proposed force field and gives the opportunity to simulate mixtures of industrial interest: a demonstration is performed through the simulation of the methyl oleate + methanol mixture involved in the purification sections of biodiesel production processes.

  15. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given.

  16. The scaled-charge additive force field for amino acid based ionic liquids

    DEFF Research Database (Denmark)

    Fileti, E. E.; Chaban, V. V.

    2014-01-01

    Ionic liquids (ILs) constitute an emerging research field. New ILs involve more and more organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their evolutional connection to proteins. We report a new non-polarizable force field (FF) for the eight AAILs com...... the CHARMM36 FF with minor modifications. Compatibility between our parameters and CHARMM36 parameters is preserved. (C) 2014 Elsevier B.V. All rights reserved....

  17. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.

    Science.gov (United States)

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments.

  18. A New Force-Matched Reactive Force Field for Bulk Water Under Extreme Thermodynamic Conditions

    Science.gov (United States)

    Fried, Laurence; Koziol, Lucas

    2015-06-01

    A many-body classical force field is presented for water under dissociative thermodynamic conditions. The force field is optimized by force-matching to ab initio molecular dynamics (AIMD) simulations calculated with Density Functional Theory (DFT). The force field contains short-ranged central and many-body over-coordination terms, and long-range Ewald electrostatics. It is optimized and tested on water at density 1.5 g/mL and 2000 K, which is approximately 10% dissociated according to DFT. Molecular dynamics simulations closely reproduce DFT radial distribution functions, as well as the distribution of wat and dissociation products. The calculated atomic self-diffusion constants appear about 50% lower than in DFT, although precise comparison is impossible due to the short timescale accessible to AIMD (about 20 ps). The force field is also compared to ReaxFF using the CHO parameter set of Chenowith et al. ReaxFF structural and dynamical properties are in overall fair agreement with DFT, although ReaxFF water is not dissociative at these conditions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  19. IM-UFF: Extending the universal force field for interactive molecular modeling.

    Science.gov (United States)

    Jaillet, Léonard; Artemova, Svetlana; Redon, Stephane

    2017-09-05

    The universal force field (UFF) is a broadly applicable classical force field that contains parameters for almost every atom type of the periodic table. This force field is non-reactive, i.e. the topology of the system under study is considered as fixed and no creation or breaking of covalent bonds is possible. This paper introduces interactive modeling-UFF (IM-UFF), an extension of UFF that combines the possibility to significantly modify molecular structures (as with reactive force fields) with a broad diversity of supported systems thanks to the universality of UFF. Such an extension lets the user easily build and edit molecular systems interactively while being guided by physics based inter-atomic forces. This approach introduces weighted atom types and weighted bonds, used to update topologies and atom parameterizations at every time step of a simulation. IM-UFF has been evaluated on a large set of benchmarks and is proposed as a self-contained implementation integrated in a new module for the SAMSON software platform for computational nanoscience available at http://www.samson-connect.net. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Toward a Broadly Applicable Force Field for d(6)-Piano Stool Complexes.

    Science.gov (United States)

    Schmid, Maurus H; Ward, Thomas R; Meuwly, Markus

    2013-05-14

    Three-legged piano stool complexes are prototypical organometallic complexes relevant to a wide range of chemically relevant questions. Force field parametrization of transition-metal complexes is difficult and underdeveloped, and metal-specific force fields and software are required. Here we report our efforts to derive parameters for the conventional CHARMM and the Valbond-CHARMM force fields for d(6)-piano stool complexes. In Valbond-CHARMM, the usual angular term is replaced with hybrid orbital strength functions. These functions describe the energy not only of distorted bond angles around the minimum but also at very large distortions. Structure optimizations led to a good agreement between the calculated force field and the X-ray structures. They were comparable to RMSDs obtained between X-ray and DFT structures. In addition, and contrary to treating the systems with DFT, molecular dynamics simulations on the multiple nanosecond time scale are possible and allow to compute meaningful structural and energetic observables. Explicit solvent simulations of the complexes in methanol and water allow to determine the solvent distribution around the complexes. The parametrization presented here will be a useful starting point for dynamics investigations of catalysts in structurally more demanding environments.

  1. Application of Pfortran and Co-Array Fortran in the Parallelization of the GROMOS96 Molecular Dynamics Module

    Directory of Open Access Journals (Sweden)

    Piotr Bała

    2001-01-01

    Full Text Available After at least a decade of parallel tool development, parallelization of scientific applications remains a significant undertaking. Typically parallelization is a specialized activity supported only partially by the programming tool set, with the programmer involved with parallel issues in addition to sequential ones. The details of concern range from algorithm design down to low-level data movement details. The aim of parallel programming tools is to automate the latter without sacrificing performance and portability, allowing the programmer to focus on algorithm specification and development. We present our use of two similar parallelization tools, Pfortran and Cray's Co-Array Fortran, in the parallelization of the GROMOS96 molecular dynamics module. Our parallelization started from the GROMOS96 distribution's shared-memory implementation of the replicated algorithm, but used little of that existing parallel structure. Consequently, our parallelization was close to starting with the sequential version. We found the intuitive extensions to Pfortran and Co-Array Fortran helpful in the rapid parallelization of the project. We present performance figures for both the Pfortran and Co-Array Fortran parallelizations showing linear speedup within the range expected by these parallelization methods.

  2. Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.

    Science.gov (United States)

    Bradshaw, Richard T; Essex, Jonathan W

    2016-08-09

    Hydration free energy (HFE) calculations are often used to assess the performance of biomolecular force fields and the quality of assigned parameters. The AMOEBA polarizable force field moves beyond traditional pairwise additive models of electrostatics and may be expected to improve upon predictions of thermodynamic quantities such as HFEs over and above fixed-point-charge models. The recent SAMPL4 challenge evaluated the AMOEBA polarizable force field in this regard but showed substantially worse results than those using the fixed-point-charge GAFF model. Starting with a set of automatically generated AMOEBA parameters for the SAMPL4 data set, we evaluate the cumulative effects of a series of incremental improvements in parametrization protocol, including both solute and solvent model changes. Ultimately, the optimized AMOEBA parameters give a set of results that are not statistically significantly different from those of GAFF in terms of signed and unsigned error metrics. This allows us to propose a number of guidelines for new molecule parameter derivation with AMOEBA, which we expect to have benefits for a range of biomolecular simulation applications such as protein-ligand binding studies.

  3. The harmonic force field and vibrational spectra of pyrrole

    Science.gov (United States)

    Xie, Yaoming; Fan, Kangnian; Boggs, James E.

    The complete harmonic vibrational force field of pyrrole has been calculated by the ab initio gradient method at the Hartree-Fock level using the 4-21 basis set. The force field was then scaled with a set of six factors transferred from benzene, and the vibrational spectrum of pyrrole was calculated. This a priori prediction, made with no reference to observations on pyrrole, agreed with the known experimental fundamental frequencies with a mean deviation of 12 cm-1 for in-plane modes and 20 cm-1 for out-of-plane modes except for the NH wagging and NH stretch. A new set of ten scale factors was next obtained by direct fitting of the computed force field to the observed pyrrole spectrum, producing the best force field obtainable by combined use of the theoretical and experimental information. This force field reproduced the entire pyrrole spectrum with mean deviations of 4·2 cm-1 (in-plane) and 5·9 cm-1 (out-of-plane). The spectra of three deuterated forms of pyrrole were also computed. Infrared absorption intensities were calculated and proved very useful in examining assignments of the two ring torsional modes and the CH stretching modes.

  4. Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

    DEFF Research Database (Denmark)

    Voroshylova, I. V.; Chaban, V. V.

    2014-01-01

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis......(trifluoromethanesulfonyl)imide, dicyanamide, hexafluorophosphate, triflate, chloride). We elaborate a systematic procedure, which allows accounting for specific cationanion interactions in the liquid phase. Once these interactions are described accurately, all experimentally determined transport properties can be reproduced. We prove...

  5. Solvation structure and dynamics of Ni{sup 2+}(aq) from a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Mareš, Jiří, E-mail: jiri.mares@oulu.fi; Vaara, Juha

    2014-10-31

    Highlights: • We parameterize the Ni{sup 2+} ion within the AMOEBA polarizable forcefield. • Besides vdW parameters, we fit also polarizability, Thole damping and charge. • We use an empirical adjustment to account for the transition into condensed phase. • Very good structural and dynamical properties of Ni{sup 2+}(aq) are demonstrated. - Abstract: An aqueous solution of Ni{sup 2+} has often been used as a prototypic transition-metal system for experimental and theoretical studies in nuclear and electron-spin magnetic resonance (NMR and ESR). Molecular dynamics (MD) simulation of Ni{sup 2+}(aq) has been a part of many of these studies. As a transition metal complex, its MD simulation is particularly difficult using common force fields. In this work, we parameterize the Ni{sup 2+} ion for a simulation of the aqueous solution within the modern polarizable force field AMOEBA. We show that a successful parameterization is possible for this specific case when releasing the physical interpretation of the electrostatic and polarization parameters of the force field. In doing so, particularly the Thole damping parameter and also the ion charge and polarizability were used as fitting parameters. The resulting parameterizations give in a MD simulation good structural and dynamical properties of the [Ni(H{sub 2}O){sub 6}]{sup 2+} complex, along with the expected excellent performance of AMOEBA for the water solvent. The presented parameterization is appropriate for high-accuracy simulations of both structural and dynamic properties of Ni{sup 2+}(aq). This work documents possible approaches of parameterization of a transition metal within the AMOEBA force field.

  6. Optimized atomistic force fields for aqueous solutions of Magnesium and Calcium Chloride: Analysis, achievements and limitations

    Science.gov (United States)

    Elfgen, Roman; Hülsmann, Marco; Krämer, Andreas; Köddermann, Thorsten; Kirschner, Karl N.; Reith, Dirk

    2016-10-01

    Molecular simulations are an important tool in the study of aqueous salt solutions. To predict the physical properties accurately and reliably, the molecular models must be tailored to reproduce experimental data. In this work, a combination of recent global and local optimization tools is used to derive force fields for MgCl2 (aq) and CaCl2 (aq). The molecular models for the ions are based on a Lennard-Jones (LJ) potential with a superimposed point charge. The LJ parameters are adjusted to reproduce the bulk density and shear viscosity of the different solutions at 1 bar and temperatures of 293.15, 303.15, and 318.15 K. It is shown that the σ-value of chloride consistently has the strongest influence on the system properties. The optimized force field for MgCl2 (aq) provides both properties in good agreement with the experimental data over a wide range of salt concentrations. For CaCl2 (aq), a compromise was made between the bulk density and shear viscosity, since reproducing the two properties requires two different choices of the LJ parameters. This is demonstrated by studying metamodels of the simulated data, which are generated to visualize the correlation between the parameters and observables by using projection plots. Consequently, in order to derive a transferable force field, an error of ˜3% on the bulk density has to be tolerated to yield the shear viscosity in satisfactory agreement with experimental data.

  7. Optimization of the OPLS-AA Force Field for Long Hydrocarbons.

    Science.gov (United States)

    Siu, Shirley W I; Pluhackova, Kristyna; Böckmann, Rainer A

    2012-04-10

    The all-atom optimized potentials for liquid simulations (OPLS-AA) force field is a popular force field for simulating biomolecules. However, the current OPLS parameters for hydrocarbons developed using short alkanes cannot reproduce the liquid properties of long alkanes in molecular dynamics simulations. Therefore, the extension of OPLS-AA to (phospho)lipid molecules required for the study of biological membranes was hampered in the past. Here, we optimized the OPLS-AA force field for both short and long hydrocarbons. Following the framework of the OPLS-AA parametrization, we refined the torsional parameters for hydrocarbons by fitting to the gas-phase ab initio energy profiles calculated at the accurate MP2/aug-cc-pVTZ theory level. Additionally, the depth of the Lennard-Jones potential for methylene hydrogen atoms was adjusted to reproduce the densities and the heats of vaporization of alkanes and alkenes of different lengths. Optimization of partial charges finally allowed to reproduce the gel-to-liquid-phase transition temperature for pentadecane and solvation free energies. It is shown that the optimized parameter set (L-OPLS) yields improved hydrocarbon diffusion coefficients, viscosities, and gauche-trans ratios. Moreover, its applicability for lipid bilayer simulations is shown for a GMO bilayer in its liquid-crystalline phase.

  8. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...

  9. Martini Coarse-Grained Force Field : Extension to DNA

    NARCIS (Netherlands)

    Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.

    2015-01-01

    We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nudeobas

  10. Martini Coarse-Grained Force Field : Extension to Carbohydrates

    NARCIS (Netherlands)

    Lopez, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Huenenberger, Philippe H.; Marrink, Siewert J.

    2009-01-01

    We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The

  11. Martini Coarse-Grained Force Field : Extension to DNA

    NARCIS (Netherlands)

    Uusitalo, Jaakko J.; Ingolfsson, Helgi I.; Akhshi, Parisa; Tieleman, D. Peter; Marrink, Siewert J.

    2015-01-01

    We systematically parameterized a coarsegrained (CG) model for DNA that is compatible with the Martini force field. The model maps each nucleotide into six to seven CG beads and is parameterized following the Martini philosophy. The CG nonbonded interactions are based on partitioning of the nudeobas

  12. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

    Science.gov (United States)

    He, Xibing; Lopes, Pedro E M; Mackerell, Alexander D

    2013-10-01

    A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments resulting in significant improvement in the treatment of the conformational energies and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules.

  13. Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields

    CERN Document Server

    Rudzinski, Joseph F

    2016-01-01

    The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent, dynamics. In this work, we rely on Markov state models to simultaneously characterize the static and kinetic properties of two CG peptide force fields---one top-down and one bottom-up. Instead of a rigorous evolution of CG dynamics (e.g., using a generalized Langevin equation), we attempt to improve the description of kinetics by simply altering the existing CG models, which employ standard Langevin dynamics. By varying masses and relevant force-field parameters, we can improve the timescale separation of the slow kinetic processes, achieve a more consistent ratio of mean-first-passage times between metastable states, and refine the relative free-energies between these states. Importantly, we show that the incorporation of kinetic information into a structure-based parametriz...

  14. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  15. Rational design of ion force fields based on thermodynamic solvation properties.

    Science.gov (United States)

    Horinek, Dominik; Mamatkulov, Shavkat I; Netz, Roland R

    2009-03-28

    Most aqueous biological and technological systems contain solvated ions. Atomistic explicit-water simulations of ionic solutions rely crucially on accurate ionic force fields, which contain most commonly two adjustable parameters: the Lennard-Jones diameter and the interaction strength. Assuming these parameters to be properly optimized, the plethora of parameters one finds in the literature for one and the same ion is surprising. In principle, the two parameters should be uniquely determined by matching two ionic properties obtained for a particular water model and within a given simulation protocol with the corresponding experimental observables. Traditionally, ion parameters were chosen in a somewhat unsystematic way to reproduce the solvation free energy and to give the correct ion size when compared with scattering results. Which experimental observable one chooses to reproduce should in principle depend on the context within which the ionic force field is going to be used. In the present work we suggest to use the solvation free energy in conjunction with the solvation entropy to construct thermodynamically sound force fields for the alkali and halide ions for the simulation of ion-specific effects in aqueous environment. To that end we determine the solvation free energy and entropy of both cations and anions in the entire relevant parameter space. As an independent check on the quality of the resulting force fields we also determine the effective ionic radius from the first peak of the radial ion-water distribution function. Several difficulties during parameter optimization are discussed in detail. (i) Single-ion solvation depends decisively on water-air surface properties, which experimentally becomes relevant when introducing extrathermodynamic assumptions on the hydronium (H(3)O(+)) solvation energy. Fitting ion pairs circumvents this problem but leaves the parameters of one reference ion (here we choose chloride) undetermined. (ii) For the halides the

  16. QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

    Science.gov (United States)

    Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

    2015-05-15

    QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.

  17. ForceFit: a code to fit classical force fields to quantum mechanical potential energy surfaces.

    Science.gov (United States)

    Waldher, Benjamin; Kuta, Jadwiga; Chen, Samuel; Henson, Neil; Clark, Aurora E

    2010-09-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. Copyright 2010 Wiley Periodicals, Inc.

  18. Machine Learning of Accurate Energy-Conserving Molecular Force Fields

    CERN Document Server

    Chmiela, Stefan; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert

    2016-01-01

    Using conservation of energy -- a fundamental property of closed classical and quantum mechanical systems -- we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/{\\AA} for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations...

  19. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...... of this variation is due to changes in the enzyme structure at distances more than 5 Å from the active site. There are significant differences between the results obtained by pure quantum methods and those from mixed quantum and molecular mechanics methods....

  20. Structural and dynamic properties of liquid tin from a new modified embedded-atom method force field

    Science.gov (United States)

    Vella, Joseph R.; Chen, Mohan; Stillinger, Frank H.; Carter, Emily A.; Debenedetti, Pablo G.; Panagiotopoulos, Athanassios Z.

    2017-02-01

    A new modified embedded-atom method (MEAM) force field is developed for liquid tin. Starting from the Ravelo and Baskes force field [Phys. Rev. Lett. 79, 2482 (1997), 10.1103/PhysRevLett.79.2482], the parameters are adjusted using a simulated annealing optimization procedure in order to obtain better agreement with liquid-phase data. The predictive capabilities of the new model and the Ravelo and Baskes force field are evaluated using molecular dynamics by comparing to a wide range of first-principles and experimental data. The quantities studied include crystal properties (cohesive energy, bulk modulus, equilibrium density, and lattice constant of various crystal structures), melting temperature, liquid structure, liquid density, self-diffusivity, viscosity, and vapor-liquid surface tension. It is shown that although the Ravelo and Baskes force field generally gives better agreement with the properties related to the solid phases of tin, the new MEAM force field gives better agreement with liquid tin properties.

  1. Molecular simulations of primary alkanolamines using an extendable force field.

    Science.gov (United States)

    Simond, Mickaël R; Ballerat-Busserolles, Karine; Coxam, Jean-Yves; Pádua, Agílio A H

    2012-12-07

    A classical force field is proposed for the molecular simulation of primary alkanolamines containing a NH(2)-C-C-OH backbone. A method is devised to take into account the polar (H-bonding) environment of the alkanolamines by calculating electrostatic charges in the presence of explicit solvent molecules. The force field does not use a universal set of charges, but is rather constructed by following a general method for obtaining specific charges for the different alkanolamines. The model is parameterized on the two simplest primary alkanolamines and then validated by calculating thermodynamic properties of five other molecules. Experimental liquid densities and enthalpies of vaporization are also reported in order to complete existing literature data. The predicted ability of the force field is evaluated by comparing the simulation results with experimental densities and enthalpies of vaporization. Densities are predicted with an uncertainty of 1.5 % and enthalpies of vaporization with an uncertainty of 1 kJ mol(-1). A decomposition of the interaction energy into electrostatic and repulsive-dispersive interactions and an analysis of hydrogen-bond statistics lead to a complex picture. Some terms of these interactions are related to the molecular structure in a clear way, others are not. The results provide insights into the structure-property relations that contribute to a better description of the thermodynamic properties of alkanolamines.

  2. Machine learning of accurate energy-conserving molecular force fields

    Science.gov (United States)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

    2017-01-01

    Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

  3. Accurate Force Field Development for Modeling Conjugated Polymers.

    Science.gov (United States)

    DuBay, Kateri H; Hall, Michelle Lynn; Hughes, Thomas F; Wu, Chuanjie; Reichman, David R; Friesner, Richard A

    2012-11-13

    The modeling of the conformational properties of conjugated polymers entails a unique challenge for classical force fields. Conjugation imposes strong constraints upon bond rotation. Planar configurations are favored, but the concomitantly shortened bond lengths result in moieties being brought into closer proximity than usual. The ensuing steric repulsions are particularly severe in the presence of side chains, straining angles, and stretching bonds to a degree infrequently found in nonconjugated systems. We herein demonstrate the resulting inaccuracies by comparing the LMP2-calculated inter-ring torsion potentials for a series of substituted stilbenes and bithiophenes to those calculated using standard classical force fields. We then implement adjustments to the OPLS-2005 force field in order to improve its ability to model such systems. Finally, we show the impact of these changes on the dihedral angle distributions, persistence lengths, and conjugation length distributions observed during molecular dynamics simulations of poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV) and poly 3-hexylthiophene (P3HT), two of the most widely used conjugated polymers.

  4. ForceFit: a code to fit classical force fields to ab-initio potential energy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Henson, Neil Jon [Los Alamos National Laboratory; Waldher, Benjamin [WSU; Kuta, Jadwiga [WSU; Clark, Aurora [WSU; Clark, Aurora E [NON LANL

    2009-01-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under Unix and is written in C++, is an easy to use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.

  5. ForceFit: a code to fit classical force fields to ab-initio potential energy surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Henson, Neil Jon [Los Alamos National Laboratory; Waldher, Benjamin [WSU; Kuta, Jadwiga [WSU; Clark, Aurora [WSU; Clark, Aurora E [NON LANL

    2009-01-01

    The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under Unix and is written in C++, is an easy to use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program.

  6. A hierarchical Bayesian framework for force field selection in molecular dynamics simulations.

    Science.gov (United States)

    Wu, S; Angelikopoulos, P; Papadimitriou, C; Moser, R; Koumoutsakos, P

    2016-02-13

    We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

  7. The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

    Science.gov (United States)

    Shi, Yue; Xia, Zhen; Zhang, Jiajing; Best, Robert; Wu, Chuanjie; Ponder, Jay W; Ren, Pengyu

    2013-01-01

    Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic multipole electrostatic parameters for each amino acid residue type are derived from high-level gas phase quantum mechanical calculations via a consistent and extensible protocol. Molecular polarizability is modeled via a Thole-style damped interactive induction model based upon distributed atomic polarizabilities. Inter- and intramolecular polarization is treated in a consistent fashion via the Thole model. The intramolecular polarization model ensures transferability of electrostatic parameters among different conformations, as demonstrated by the agreement between QM and AMOEBA electrostatic potentials, and dipole moments of dipeptides. The backbone and side chain torsional parameters were determined by comparing to gas-phase QM (RI-TRIM MP2/CBS) conformational energies of dipeptides and to statistical distributions from the Protein Data Bank. Molecular dynamics simulations are reported for short peptides in explicit water to examine their conformational properties in solution. Overall the calculated conformational free energies and J-coupling constants are consistent with PDB statistics and experimental NMR results, respectively. In addition, the experimental crystal structures of a number of proteins are well maintained during molecular dynamics (MD) simulation. While further calculations are necessary to fully validate the force field, initial results suggest the AMOEBA polarizable multipole force field is able to describe the structure and energetics of peptides and proteins, in both gas-phase and solution environments.

  8. Multiscale modeling of drug-polymer nanoparticle assembly identifies parameters influencing drug encapsulation efficiency.

    Science.gov (United States)

    Mackenzie, R; Booth, J; Alexander, C; Garnett, M C; Laughton, C A

    2015-06-09

    Using a multiscale (dual resolution) approach combining an atomistic (GROMOS96) and coarse-grain (MARTINI) force field, we have been able to simulate the process of drug-polymer nanoparticle assembly by nanoprecipitation from mixed solvents. Here, we present the development and application of this method to the interaction of three poly(glycerol adipate) polymer variants with the anticancer drug dexamethasone phosphate. Differences in encapsulation efficiency and drug loading between the polymers are in agreement with the experimental trend. Reference atomistic simulations at key points along the predicted aggregation pathway support the accuracy of the much more computationally efficient multiscale methodology.

  9. Hexamethylenetetramine (urotropine) C6H12N2: Interpreting the vibrational spectra of -d0 and -d12 isotopomers by scaling the quantum-chemical force field

    Science.gov (United States)

    Khaikin, L. S.; Grikina, O. E.; Kochikov, I. V.; Stepanov, N. F.

    2014-03-01

    The equilibrium structure and quadratic and cubic force fields of the urotropine molecule are calculated at the MP2 (full)/cc-pVTZ level. Pulay scaling of the quadratic force field allows unambiguous interpretation of the vibrational spectra of -d0 and -d12 urotropines. A reliable matrix for the quadratic force constants of urotropine is obtained which may be used to determine the parameters of the equilibrium structure of the urotropine molecule by means of gas-phase electron diffraction.

  10. Atomistic force field for alumina fit to density functional theory.

    Science.gov (United States)

    Sarsam, Joanne; Finnis, Michael W; Tangney, Paul

    2013-11-28

    We present a force field for bulk alumina (Al2O3), which has been parametrized by fitting the energies, forces, and stresses of a large database of reference configurations to those calculated with density functional theory (DFT). We use a functional form that is simpler and computationally more efficient than some existing models of alumina parametrized by a similar technique. Nevertheless, we demonstrate an accuracy of our potential that is comparable to those existing models and to DFT. We present calculations of crystal structures and energies, elastic constants, phonon spectra, thermal expansion, and point defect formation energies.

  11. Spatial Confinement of Ultrasonic Force Fields in Microfluidic Channels

    DEFF Research Database (Denmark)

    Manneberg, O; Hagsäter, Melker; Svennebring, J;

    2009-01-01

    of the microfluidic channel. The channel segments are remotely actuated by the use of frequency-specific external transducers with refracting wedges placed on top of the chips. The force field in each channel segment is characterized by the use of micrometer-resolution particle image velocimetry ( micro......-PIV). The confinement of the ultrasonic fields during single-or dual-segment actuation, as well as the cross-talk between two adjacent. fields, is characterized and quantified. Our results show that the field confinement typically scales with the acoustic wavelength, and that the cross-talk is insignificant between...

  12. Vibrational Spectra of the Azabenzenes Revisited: Anharmonic Force Fields

    CERN Document Server

    Boese, A D; Martin, Jan M.L.

    2003-01-01

    Anharmonic force fields and vibrational spectra of the azabenzene series (pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, 1,2,3-triazine, 1,2,4-triazine and s-tetrazine) and benzene are obtained using density functional theory (DFT) with the B97-1 exchange-correlation functional and a triple-zeta plus double polarization (TZ2P) basis set. Overall, the fundamental frequencies computed by second-order rovibrational perturbation theory are in excellent agreement with experiment. The resolution of the presently calculated anharmonic spectra is such that they represent an extremely useful tool for the assignment and interpretation of the experimental spectra, especially where resonances are involved.

  13. Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem.

    Science.gov (United States)

    Hopkins, Chad W; Roitberg, Adrian E

    2014-07-28

    The derivation and optimization of most energy terms in modern force fields are aided by automated computational tools. It is therefore important to have algorithms to rapidly and precisely train large numbers of interconnected parameters to allow investigators to make better decisions about the content of molecular models. In particular, the traditional approach to deriving dihedral parameters has been a least-squares fit to target conformational energies through variational optimization strategies. We present a computational approach for simultaneously fitting force field dihedral amplitudes and phase constants which is analytic within the scope of the data set. This approach completes the optimal molecular mechanics representation of a quantum mechanical potential energy surface in a single linear least-squares fit by recasting the dihedral potential into a linear function in the parameters. We compare the resulting method to a genetic algorithm in terms of computational time and quality of fit for two simple molecules. As suggested in previous studies, arbitrary dihedral phases are only necessary when modeling chiral molecules, which include more than half of drugs currently in use, so we also examined a dihedral parametrization case for the drug amoxicillin and one of its stereoisomers where the target dihedral includes a chiral center. Asymmetric dihedral phases are needed in these types of cases to properly represent the quantum mechanical energy surface and to differentiate between stereoisomers about the chiral center.

  14. Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

    Science.gov (United States)

    Chapman, Dail E; Steck, Jonathan K; Nerenberg, Paul S

    2014-01-14

    The quality of molecular dynamics (MD) simulations relies heavily on the accuracy of the underlying force field. In recent years, considerable effort has been put into developing more accurate dihedral angle potentials for MD force fields, but relatively little work has focused on the nonbonded parameters, many of which are two decades old. In this work, we assess the accuracy of protein-protein van der Waals interactions in the AMBER ff9x/ff12 force field. Across a test set of 44 neat organic liquids containing the moieties present in proteins, we find root-mean-square (RMS) errors of 1.26 kcal/mol in enthalpy of vaporization and 0.36 g/cm(3) in liquid densities. We then optimize the van der Waals radii and well depths for all of the relevant atom types using these observables, which lowers the RMS errors in enthalpy of vaporization and liquid density of our validation set to 0.59 kcal/mol (53% reduction) and 0.019 g/cm(3) (46% reduction), respectively. Limitations in our parameter optimization were evident for certain atom types, however, and we discuss the implications of these observations for future force field development.

  15. Molecular force fields for aqueous electrolytes: SPC/E-compatible charged LJ sphere models and their limitations.

    Science.gov (United States)

    Moučka, Filip; Nezbeda, Ivo; Smith, William R

    2013-04-21

    Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012)]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.

  16. Force-field compensation in a manual tracking task.

    Directory of Open Access Journals (Sweden)

    Valentina Squeri

    Full Text Available This study addresses force/movement control in a dynamic "hybrid" task: the master sub-task is continuous manual tracking of a target moving along an eight-shaped Lissajous figure, with the tracking error as the primary performance index; the slave sub-task is compensation of a disturbing curl viscous field, compatibly with the primary performance index. The two sub-tasks are correlated because the lateral force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%, which is a function of the implicit accuracy of the tracking task.

  17. Active contour model based on force field analysis

    Institute of Scientific and Technical Information of China (English)

    HOU Zhi-qiang; HAN Chong-zhao

    2006-01-01

    The traditional snake initial contour should be close to the true boundary of an object of interest in an image;otherwise,an incorrect result will be obtained.Next,active contours have difficulties progressing into boundary concavities.Moreover,the traditional snake as well as almost all of its improved methods can be easily obtained from the local minimum because snake models are nonconvex.An active contour model based on force field analysis (FFA),namely,FFA snake model,is presented in this paper.Based on analyzing force distribution rules of the distance potential force field,a standard is introduced here to distinguish the false one from contour points.The result is not considered as the final solution when the snake energy is minimal.Furthermore,estimation and calculation should be made according to the established standard;only then can the result be considered final.Thus,the snake is prevented from running into the local minimum.The simulation results show that the FFA snake model has a large capture range and can move a snake into the boundary concavities,and that it is able to obtain the object of interest's contour precisely.Compared with the gradient vector flow snake,this new model has a low computational cost.

  18. The Quantum Space Phase Transitions for Particles and Force Fields

    Directory of Open Access Journals (Sweden)

    Chung D.-Y.

    2006-07-01

    Full Text Available We introduce a phenomenological formalism in which the space structure is treated in terms of attachment space and detachment space. Attachment space attaches to an object, while detachment space detaches from the object. The combination of these spaces results in three quantum space phases: binary partition space, miscible space and binary lattice space. Binary lattice space consists of repetitive units of alternative attachment space and detachment space. In miscible space, attachment space is miscible to detachment space, and there is no separation between attachment space and detachment spaces. In binary partition space, detachment space and attachment space are in two separat continuous regions. The transition from wavefunction to the collapse of wavefuction under interference becomes the quantum space phase transition from binary lattice space to miscible space. At extremely conditions, the gauge boson force field undergoes a quantum space phase transition to a "hedge boson force field", consisting of a "vacuum" core surrounded by a hedge boson shell, like a bubble with boundary.

  19. A new united atom force field for adsorption of alkenes in zeolites

    NARCIS (Netherlands)

    Liu, B.; Smit, B.; Rey, F.; Valencia, S.; Calero, S.

    2008-01-01

    A new united atom force field was developed that accurately describes the adsorption properties of linear alkenes in zeolites. The force field was specifically designed for use in the inhomogeneous system and therefore a truncated and shifted potential was used. With the determined force field, we p

  20. Validating empirical force fields for molecular-level simulation of cellulose dissolution

    Science.gov (United States)

    The calculations presented here, which include dynamics simulations using analytical force fields and first principles studies, indicate that the COMPASS force field is preferred over the Dreiding and Universal force fields for studying dissolution of large cellulose structures. The validity of thes...

  1. Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC.

    Science.gov (United States)

    Sweere, Augustinus J M; Fraaije, Johannes G E M

    2017-05-09

    We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol). PAC-MAC shows a RMSE of 0.151 kBT with a calculation speed being potentially 1.0 × 10(4) times greater than TI. OPLS-AA force field parameters are optimized using PAC-MAC based on vapor-liquid equilibrium data, instead of enthalpies of vaporization or densities. The RMSE of PAC-MAC is reduced to 0.099 kBT by optimizing 50 force field parameters. The resulting OPLS-PM force field has a comparable accuracy as the OPLS-AA force field in the calculation of mixing free energies using TI.

  2. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  3. A Multiposture Locomotor Training Device with Force-Field Control

    Directory of Open Access Journals (Sweden)

    Jianfeng Sui

    2014-11-01

    Full Text Available This paper introduces a multiposture locomotor training device (MPLTD with a closed-loop control scheme based on joint angle feedback, which is able to overcome various difficulties resulting from mechanical vibration and the weight of trainer to achieve higher accuracy trajectory. By introducing the force-field control scheme used in the closed-loop control, the device can obtain the active-constrained mode including the passive one. The MPLTD is mainly composed of three systems: posture adjusting and weight support system, lower limb exoskeleton system, and control system, of which the lower limb exoskeleton system mainly includes the indifferent equilibrium mechanism with two degrees of freedom (DOF and the driving torque is calculated by the Lagrangian function. In addition, a series of experiments, the weight support and the trajectory accuracy experiment, demonstrate a good performance of mechanical structure and the closed-loop control.

  4. Combining configurational energies and forces for molecular force field optimization

    Science.gov (United States)

    Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

    2017-10-01

    While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. Here we propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information is used to optimize a molecular force field by minimizing the statistical distance similarity metric. We illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.

  5. Enthalpy of formation and anharmonic force field of diacetylene.

    Science.gov (United States)

    Simmonett, Andrew C; Schaefer, Henry F; Allen, Wesley D

    2009-01-28

    The enthalpy of formation of diacetylene (C4H2) is pinpointed using state-of-the-art theoretical methods, accounting for high-order electron correlation, relativistic effects, non-Born-Oppenheimer corrections, and vibrational anharmonicity. Molecular energies are determined from coupled cluster theory with single and double excitations (CCSD), perturbative triples [CCSD(T)], full triples (CCSDT), and perturbative quadruples [CCSDT(Q)], in concert with correlation-consistent basis sets (cc-pVXZ, X=D, T, Q, 5, 6) that facilitate extrapolations to the complete basis set limit. The first full quartic force field of diacetylene is determined at the highly accurate all-electron CCSD(T) level with a cc-pCVQZ basis, which includes tight functions for core correlation. Application of second-order vibrational perturbation theory to our anharmonic force field yields fundamental frequencies with a mean absolute difference of only 3.9 cm(-1) relative to the experimental band origins, without the use of any empirical scale factors. By a focal point approach, we converge on an enthalpy change for the isogyric reaction 2 H-C[triple bond]C-H-->H-C[triple bond]C-C[triple bond]C-H+H2 of (+0.03, +0.81) kcal mol(-1) at (0, 298.15) K. With the precisely established fHdegrees of acetylene, we thus obtain DeltafHdegrees(C4H2)=(109.4,109.7)+/-0.3 kcal mol(-1) at (0, 298.15) K. Previous estimates of the diacetylene enthalpy of formation range from 102 to 120 kcal mol(-1).

  6. Extension of the transferable potentials for phase equilibria force field to dimethylmethyl phosphonate, sarin, and soman.

    Science.gov (United States)

    Sokkalingam, Nandhini; Kamath, Ganesh; Coscione, Maria; Potoff, Jeffrey J

    2009-07-30

    The transferable potentials for phase equilibria force field is extended to dimethylmethylphosphonate (DMMP), sarin, and soman by introducing a new interaction site representing the phosphorus atom. Parameters for the phosphorus atom are optimized to reproduce the liquid densities at 303 and 373 K and the normal boiling point of DMMP. Calculations for sarin and soman are performed in predictive mode, without further parameter optimization. Vapor-liquid coexistence curves, critical properties, vapor pressures and heats of vaporization are predicted over a wide range of temperatures with histogram reweighting Monte Carlo simulations in the grand canonical ensemble. Excellent agreement with experiment is achieved for all compounds, with unsigned errors of less than 1% for vapor pressures and normal boiling points and under 5% for heats of vaporization and liquid densities at ambient conditions.

  7. A method to study precision grip control in viscoelastic force fields using a robotic gripper.

    Science.gov (United States)

    Lambercy, Olivier; Metzger, Jean-Claude; Santello, Marco; Gassert, Roger

    2015-01-01

    Instrumented objects and multipurpose haptic displays have commonly been used to investigate sensorimotor control of grasping and manipulation. A major limitation of these devices, however, is the extent to which the experimenter can vary the interaction dynamics to fully probe sensorimotor control mechanisms. We propose a novel method to study precision grip control using a grounded robotic gripper with two moving, mechanically coupled finger pads instrumented with force sensors. The device is capable of stably rendering virtual mechanical properties with a wide dynamic range of achievable impedances. Eight viscoelastic force fields with different combinations of stiffness and damping parameters were implemented, and tested on eight healthy subjects performing 30 consecutive repetitions of a grasp, hold, and release task with time and position constraints. Rates of thumb and finger force were found to be highly correlated (r>0.9) during grasping, revealing that, despite the mechanical coupling of the two finger pads, subjects performed grasping movements in a physiological fashion. Subjects quickly adapted to the virtual dynamics (within seven trials), but, depending on the presented force field condition, used different control strategies to correctly perform the task. The proof of principle presented in this paper underscores the potential of such a one-degree-of-freedom robotic gripper to study neural control of grasping, and to provide novel insights on sensorimotor control mechanisms.

  8. Minimal Basis Iterative Stockholder: Atoms in Molecules for Force-Field Development

    CERN Document Server

    Verstraelen, Toon; Heidar-Zadeh, Farnaz; Vanduyfhuys, Louis; Van Speybroeck, Veronique; Waroquier, Michel; Ayers, Paul W

    2016-01-01

    Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g. obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-sca...

  9. Modelling of Ion Transport in Solids with a General Bond Valence Based Force-Field

    Directory of Open Access Journals (Sweden)

    S. Adams

    2010-12-01

    Full Text Available Empirical bond length - bond valence relations provide insight into the link between structure of and ion transport in solid electrolytes. Building on our earlier systematic adjustment of bond valence (BV parameters to the bond softness, here we discuss how the squared BV mismatch can be linked to the absolute energy scale and used as a general Morse-type interaction potential for analyzing low-energy pathways in ion conducting solid or mixed conductors either by an energy landscape approach or by molecular dynamics (MD simulations. For a wide range of Lithium oxides we could thus model ion transport revealing significant differences to an earlier geometric approach. Our novel BV-based force-field has also been applied to investigate a range of mixed conductors, focusing on cathode materials for lithium ion battery (LIB applications to promote a systematic design of LIB cathodes that combine high energy density with high power density. To demonstrate the versatility of the new BV-based force-field it is applied in exploring various strategies to enhance the power performance of safe low cost LIB materials (LiFePO4, LiVPO4F, LiFeSO4F, etc..

  10. An optimized charge penetration model for use with the AMOEBA force field.

    Science.gov (United States)

    Rackers, Joshua A; Wang, Qiantao; Liu, Chengwen; Piquemal, Jean-Philip; Ren, Pengyu; Ponder, Jay W

    2016-12-21

    The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol(-1) to 1.3 kcal mol(-1). The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.

  11. The R.E.D. Tools: Advances in RESP and ESP charge derivation and force field library building

    Science.gov (United States)

    Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

    2010-01-01

    Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure, because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, http://q4md-forcefieldtools.org/RED/) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed. PMID:20574571

  12. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

    Science.gov (United States)

    Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

    2010-07-28

    Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

  13. Results from the validation campaign of the ozone radiometer GROMOS-C at the NDACC station of Réunion island

    Science.gov (United States)

    Fernandez, Susana; Rüfenacht, Rolf; Kämpfer, Niklaus; Portafaix, Thierry; Posny, Françoise; Payen, Guillaume

    2016-06-01

    Ozone performs a key role in the middle atmosphere and its monitoring is thus necessary.At the Institute of Applied Physics of the University of Bern, Switzerland, we built a new ground-based microwave radiometer, GROMOS-C (GRound based Ozone MOnitoring System for Campaigns). It has a compact design and can be operated remotely with very little maintenance requirements, being therefore suitable for remote deployments. It has been conceived to measure the vertical distribution of ozone in the middle atmosphere, by observing pressure-broadened emission spectra at a frequency of 110.836 GHz. In addition, meridional and zonal wind profiles can be retrieved, based on the Doppler shift of the ozone line measured in the four directions of observation (north, east, south and west).In June 2014 the radiometer was installed at the Maïdo observatory, on Réunion island (21.2° S, 55.5° E). High-resolution ozone spectra were recorded continuously over 7 months. Vertical profiles of ozone have been retrieved through an optimal estimation inversion process, using the Atmospheric Radiative Transfer Simulator ARTS2 as the forward model. The validation is performed against ozone profiles from the Microwave Limb Sounder (MLS) on the Aura satellite, the ozone lidar located at the observatory and with ozone profiles from weekly radiosondes. Zonal and meridional winds retrieved from GROMOS-C data are validated against another wind radiometer located in situ, WIRA. In addition, we compare both ozone and winds with ECMWF (European Centre for Medium-Range Weather Forecasts) model data. Results show that GROMOS-C provides reliable ozone profiles between 30 and 0.02 hPa. The comparison with lidar profiles shows a very good agreement at all levels. The accordance with the MLS data set is within 5 % for pressure levels between 25 and 0.2 hPa. GROMOS-C's wind profiles are in good agreement with the observations by WIRA and with the model data, differences are below 5 m s-1 for both.

  14. International Acquisitons in Multinacionals: Under a Force Field

    Directory of Open Access Journals (Sweden)

    Américo da Costa Ramos Filho

    2010-12-01

    Full Text Available The purpose of this essay is to debate the performance of multinational companies concerning the management alternatives of their foreign unities, especially the ones derived from acquisitions, with consequences on the interaction between the headquarters and its subsidiaries or colligates and the managerial learning and knowledge associated to this process. First the problematic of internationalized companies by foreign direct investments – FDI’s, mainly by acquisitions and strategic alliances, is discussed. The intensity of the assimilation and interchange of values and practices within organizations in interacting process is stressed, including a set of typologies derived from the existing related literature. After this, a more specific approach about intra and interorganization aspects of the multinationals is performed, related to strategies, competences and roles of headquarters and subsidiaries, as well as their impact on the knowledge flux and its derived learning modes, evolving a established typologies set. The next step is to discuss two visions about the opposition between the universal and the particular in international management, with global and contextual aspects: a convergence-divergence opposition, like a force field, impacting on the knowledge transfer. Finally, some concluding comments are made, emphasizing, for the purpose of contribution, another type of multinationals typology relating the convergence-divergence duality to the organizational and national levels, as well the positioning of the companies in the resulted matrix.

  15. Accurate Interatomic Force Fields via Machine Learning with Covariant Kernels

    CERN Document Server

    Glielmo, Aldo; De Vita, Alessandro

    2016-01-01

    We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian Process (GP) Regression. This is based on matrix-valued kernel functions, to which we impose that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such "covariant" GP kernels can be obtained by integration over the elements of the rotation group SO(d) for the relevant dimensionality d. Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni and Fe crystalline...

  16. Accurate interatomic force fields via machine learning with covariant kernels

    Science.gov (United States)

    Glielmo, Aldo; Sollich, Peter; De Vita, Alessandro

    2017-06-01

    We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian process (GP) regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group SO (d ) for the relevant dimensionality d . Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe, and Si crystalline systems.

  17. Quantum mechanical force fields for condensed phase molecular simulations

    Science.gov (United States)

    Giese, Timothy J.; York, Darrin M.

    2017-09-01

    Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

  18. Mapping the force field of a hydrogen-bonded assembly

    Science.gov (United States)

    Sweetman, A. M.; Jarvis, S. P.; Sang, Hongqian; Lekkas, I.; Rahe, P.; Wang, Yu; Wang, Jianbo; Champness, N. R.; Kantorovich, L.; Moriarty, P.

    2014-05-01

    Hydrogen bonding underpins the properties of a vast array of systems spanning a wide variety of scientific fields. From the elegance of base pair interactions in DNA to the symmetry of extended supramolecular assemblies, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the hydrogen bond continue to be vigorously debated. Here we use dynamic force microscopy (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide molecules hydrogen-bonded in two-dimensional assemblies. A comparison of experimental images and force spectra with their simulated counterparts shows that intermolecular contrast arises from repulsive tip-sample interactions whose interpretation can be aided via an examination of charge density depletion across the molecular system. Interpreting DFM images of hydrogen-bonded systems therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

  19. Mapping the force-field of a hydrogen bonded assembly

    Science.gov (United States)

    Moriarty, Philip

    2014-03-01

    Hydrogen-bonding underpins the structure, properties, and dynamics of a vast array of systems spanning a wide variety of scientific fields. From the striking complexity of the phase diagram of H2O and the elegance of base pair interactions in DNA, to the directionality inherent in supramolecular self-assembly at surfaces, hydrogen bonds play an essential role in directing intermolecular forces. Yet fundamental aspects of the H-bond, including the magnitude of the force and binding energy, force constant, and decay length associated with the interaction, have been vigorously debated for many decades. I will discuss how dynamic force microscopy (DFM) using a qPlus sensor can quantitatively map the tip-sample force-field for naphthalene tetracarboxylic diimide (NTCDI) molecules hydrogen-bonded in 2D assemblies. A comparison of experimental images and force spectra with their simulated counterparts from density functional theory calculations shows that image contrast due to intermolecular hydrogen bonds arises fundamentally from charge density depletion due to strong tip-sample interactions. Interpretation of DFM images of hydrogen bonds therefore necessitates detailed consideration of the coupled tip-molecule system: analyses based on intermolecular charge density in the absence of the tip fail to capture the essential physical chemistry underpinning the imaging mechanism.

  20. Optimization of force constants with an Urey-Bradley force field avoiding normal mode crossings.

    Science.gov (United States)

    Vivoni, A; Birke, R; Lombardi, J

    2001-03-01

    We present a method that simplifies the refinement of force constants in normal mode calculations and makes the results more reliable. The method avoids normal mode crossings by constraining the force constants during refinement. It was tested with pyrrole, imidazole, benzene, pyridine, pyrimidine, aniline and adenine using a Urey-Bradley force field. The global error of the frequency fit for these molecules was 0.61%. The method reproduced with fewer parameters the accuracy of similar calculations of the single ring aromatic compounds. It improved the accuracy and isotopic shifts of previous empirical calculations of adenine by 40%. The C-C and C-N stretchings differed by less than 7% from the values of force constant-bond length empirical relations.

  1. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

    Science.gov (United States)

    Hart, Katarina; Foloppe, Nicolas; Baker, Christopher M; Denning, Elizabeth J; Nilsson, Lennart; Mackerell, Alexander D

    2012-01-10

    The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles ε and ζ (BI = ε-ζ 0). BI is the most populated state, but the population of the BII state, which is sequence dependent, is significant and accumulating evidence shows that BII affects the overall structure of DNA, and thus influences protein-DNA recognition. This work presents a reparametrization of the CHARMM27 additive nucleic acid force field to increase the sampling of the BII form in MD simulations of DNA. In addition, minor modifications of sugar puckering were introduced to facilitate sampling of the A form of DNA under the appropriate environmental conditions. Parameter optimization was guided by quantum mechanical data on model compounds, followed by calculations on several DNA duplexes in the condensed phase. The selected optimized parameters were then validated against a number of DNA duplexes, with the most extensive tests performed on the EcoRI dodecamer, including comparative calculations using the Amber Parm99bsc0 force field. The new CHARMM model better reproduces experimentally observed sampling of the BII conformation, including sampling as a function of sequence. In addition, the model reproduces the A form of the 1ZF1 duplex in 75 % ethanol, and yields a stable Z-DNA conformation of duplex (GTACGTAC) in its crystal environment. The resulting model, in combination with a recent reoptimization of the CHARMM27 force field for RNA, will be referred to as CHARMM36.

  2. Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

    DEFF Research Database (Denmark)

    Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter

    2013-01-01

    reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein...... force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector......In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously...

  3. The influence of catch trials on the consolidation of motor memory in force field adaptation tasks

    Directory of Open Access Journals (Sweden)

    Anne eFocke

    2013-07-01

    Full Text Available In computational neuroscience it is generally accepted that human motor memory contains neural representations of the physics of the musculoskeletal system and the objects in the environment. These representations are called internal models. Force field studies, in which subjects have to adapt to dynamic perturbations induced by a robotic manipulandum, are an established tool to analyze the characteristics of such internal models. The aim of the current study was to investigate whether catch trials during force field learning could influence the consolidation of motor memory in more complex tasks. Thereby, the force field was more than double the force field of previous studies (35 Ns/m. Moreover, the arm of the subjects was not supported. A total of forty-six subjects participated in this study and performed center-out movements at a robotic manipulandum in two different force fields. Two control groups learned force field A on day 1 and were retested in the same force field on day 3 (AA. Two test groups additionally learned an interfering force field B (=-A on day 2 (ABA. The difference between the two test and control groups, respectively, was the absence (0% or presence (19% of catch trials, in which the force field was turned off suddenly. The results showed consolidation of force field A on day 3 for both control groups. Test groups showed no consolidation of force field A (19% catch trials and even poorer performance on day 3 (0% catch trials. In conclusion, it can be stated that catch trials seem to have a positive effect on the performance on day 3 but do not trigger a consolidation process as shown in previous studies that used a lower force field viscosity with supported arm. These findings indicate that the results of previous studies in which less complex tasks were analyzed, cannot be fully transferred to more complex tasks. Moreover, the effects of catch trials in these situations are insufficiently understood and further research

  4. Molecular dynamics simulations of hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using a combined Sorescu-Rice-Thompson AMBER force field.

    Science.gov (United States)

    Agrawal, Paras M; Rice, Betsy M; Zheng, Lianqing; Thompson, Donald L

    2006-12-28

    We present the results of molecular dynamics simulations of crystalline hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) using the SRT-AMBER force field (P. M. Agrawal et al., J. Phys. Chem. B 2006, 110, 5721), which combines the rigid-molecule force field developed by Sorescu-Rice-Thompson (D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 1997, 101, 798) with the intramolecular interactions obtained from the Generalized AMBER Force Field (Wang et al., J. Comput. Chem. 2004, 25, 1157). The calculated crystal density at room conditions is about 10% lower than the measured value, while the lattice parameters and thermodynamic melting point are within about 5% at ambient pressure. The chair and inverted chair conformation, bond lengths, and bond angles of the RDX molecule are accurately predicted; however, there are some inaccuracies in the calculated orientations of the NO2 groups. The SRT-AMBER force field predicts overall reasonable results, but modifications, probably in the torsional parameters, are needed for a more accurate force field.

  5. Extension of the ReaxFF Combustion Force Field toward Syngas Combustion and Initial Oxidation Kinetics.

    Science.gov (United States)

    Ashraf, Chowdhury; van Duin, Adri C T

    2017-02-09

    A detailed insight of key reactive events related to oxidation and pyrolysis of hydrocarbon fuels further enhances our understanding of combustion chemistry. Though comprehensive kinetic models are available for smaller hydrocarbons (typically C3 or lower), developing and validating reaction mechanisms for larger hydrocarbons is a daunting task, due to the complexity of their reaction networks. The ReaxFF method provides an attractive computational method to obtain reaction kinetics for complex fuel and fuel mixtures, providing an accuracy approaching ab-initio-based methods but with a significantly lower computational expense. The development of the first ReaxFF combustion force field by Chenoweth et al. (CHO-2008 parameter set) in 2008 has opened new avenues for researchers to investigate combustion chemistry from the atomistic level. In this article, we seek to address two issues with the CHO-2008 ReaxFF description. While the CHO-2008 description has achieved significant popularity for studying large hydrocarbon combustion, it fails to accurately describe the chemistry of small hydrocarbon oxidation, especially conversion of CO2 from CO, which is highly relevant to syngas combustion. Additionally, the CHO-2008 description was obtained faster than expected H abstraction by O2 from hydrocarbons, thus underestimating the oxidation initiation temperature. In this study, we seek to systemically improve the CHO-2008 description and validate it for these cases. Additionally, our aim was to retain the accuracy of the 2008 description for larger hydrocarbons and provide similar quality results. Thus, we expanded the ReaxFF CHO-2008 DFT-based training set by including reactions and transition state structures relevant to the syngas and oxidation initiation pathways and retrained the parameters. To validate the quality of our force field, we performed high-temperature NVT-MD simulations to study oxidation and pyrolysis of four different hydrocarbon fuels, namely, syngas

  6. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

    Science.gov (United States)

    Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

    2017-02-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (uc(d)-allose and uc(d)-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars uc(d)-allose and uc(d)-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  7. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

    Science.gov (United States)

    Small, Meagan C.; Aytenfisu, Asaminew H.; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D.

    2017-04-01

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars ( d-allose and d-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars d-allose and d-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  8. Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates.

    Science.gov (United States)

    Small, Meagan C; Aytenfisu, Asaminew H; Lin, Fang-Yu; He, Xibing; MacKerell, Alexander D

    2017-02-11

    The majority of computer simulations exploring biomolecular function employ Class I additive force fields (FF), which do not treat polarization explicitly. Accordingly, much effort has been made into developing models that go beyond the additive approximation. Development and optimization of the Drude polarizable FF has yielded parameters for selected lipids, proteins, DNA and a limited number of carbohydrates. The work presented here details parametrization of aliphatic aldehydes and ketones (viz. acetaldehyde, propionaldehyde, butaryaldehyde, isobutaryaldehyde, acetone, and butanone) as well as their associated acyclic sugars (D-allose and D-psicose). LJ parameters are optimized targeting experimental heats of vaporization and molecular volumes, while the electrostatic parameters are optimized targeting QM water interactions, dipole moments, and molecular polarizabilities. Bonded parameters are targeted to both QM and crystal survey values, with the models for ketones and aldehydes shown to be in good agreement with QM and experimental target data. The reported heats of vaporization and molecular volumes represent a compromise between the studied model compounds. Simulations of the model compounds show an increase in the magnitude and the fluctuations of the dipole moments in moving from gas phase to condensed phases, which is a phenomenon that the additive FF is intrinsically unable to reproduce. The result is a polarizable model for aliphatic ketones and aldehydes including the acyclic sugars D-allose and D-psicose, thereby extending the available biomolecules in the Drude polarizable FF.

  9. Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

    Energy Technology Data Exchange (ETDEWEB)

    MacDermaid, Christopher M., E-mail: chris.macdermaid@temple.edu; Klein, Michael L.; Fiorin, Giacomo, E-mail: giacomo.fiorin@temple.edu [Institute for Computational Molecular Science, Temple University, 1925 North 12th Street, Philadelphia, Pennsylvania 19122-1801 (United States); Kashyap, Hemant K. [Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); DeVane, Russell H. [Modeling and Simulation, Corporate Research and Development, The Procter and Gamble Company, West Chester, Ohio 45069 (United States); Shinoda, Wataru [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Klauda, Jeffery B. [Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

    2015-12-28

    The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.

  10. Simulating GTP:Mg and GDP:Mg with a simple force field: a structural and thermodynamic analysis.

    Science.gov (United States)

    Simonson, Thomas; Satpati, Priyadarshi

    2013-04-05

    Di- and tri-phosphate nucleotides are essential cofactors for many proteins, usually in an Mg(2+) -bound form. Proteins like GTPases often detect the difference between NDP and NTP and respond by changing conformations. To study such complexes, simple, fixed charge force fields have been used, which allow long simulations and precise free energy calculations. The preference for NTP or NDP binding depends on many factors, including ligand structure and Mg(2+) coordination and the changes they undergo upon binding. Here, we use a simple force field to examine two Mg(2+) coordination modes for the unbound GDP and GTP: direct, or "Inner Sphere" (IS) coordination by one or more phosphate oxygens and indirect, "Outer Sphere" (OS) coordination involving one or more bridging waters. We compare GTP: and GDP:Mg binding with OS and IS coordination; combining the results with experimental data then indicates that GTP prefers the latter. We also examine different kinds of IS coordination and their sensitivity to a key force field parameter: the optimal Mg:oxygen van der Waals distance Rmin . Increasing Rmin improves the Mg:oxygen distances, the GTP: and GDP:Mg binding affinities, and the fraction of GTP:Mg with β + γ phosphate coordination, but does not improve or change the GTP/GDP affinity difference, which remains much larger than experiment. It has no effect on the free energy of GDP binding to a GTPase. Copyright © 2012 Wiley Periodicals, Inc.

  11. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

    Science.gov (United States)

    Tran, Thanh Thuy; Nguyen, Phuong H.; Derreumaux, Philippe

    2016-05-01

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  12. High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

    Science.gov (United States)

    Tian, Ye; Schwieters, Charles D; Opella, Stanley J; Marassi, Francesca M

    2017-01-01

    Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision

  13. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field

    NARCIS (Netherlands)

    García-Pérez, E.; Serra-Crespo,P.; Hamad, S.; Kapteijn, F.; Gascon, J.

    2014-01-01

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations o

  14. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field

    NARCIS (Netherlands)

    García-Pérez, E.; Serra-Crespo,P.; Hamad, S.; Kapteijn, F.; Gascon, J.

    2014-01-01

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations

  15. Artificial force fields for multi-agent simulations of maritime traffic and risk estimation

    NARCIS (Netherlands)

    Xiao, F.; Ligteringen, H.; Van Gulijk, C.; Ale, B.J.M.

    2012-01-01

    A probabilistic risk model is designed to estimate probabilities of collisions for shipping accidents in busy waterways. We propose a method based on multi-agent simulation that uses an artificial force field to model ship maneuvers. The artificial force field is calibrated by AIS data (Automatic Id

  16. Distinct haptic cues do not reduce interference when learning to reach in multiple force fields.

    Directory of Open Access Journals (Sweden)

    Nicholas Cothros

    Full Text Available BACKGROUND: Previous studies of learning to adapt reaching movements in the presence of novel forces show that learning multiple force fields is prone to interference. Recently it has been suggested that force field learning may reflect learning to manipulate a novel object. Within this theoretical framework, interference in force field learning may be the result of static tactile or haptic cues associated with grasp, which fail to indicate changing dynamic conditions. The idea that different haptic cues (e.g. those associated with different grasped objects signal motor requirements and promote the learning and retention of multiple motor skills has previously been unexplored in the context of force field learning. METHODOLOGY/PRINCIPLE FINDINGS: The present study tested the possibility that interference can be reduced when two different force fields are associated with differently shaped objects grasped in the hand. Human subjects were instructed to guide a cursor to targets while grasping a robotic manipulandum, which applied two opposing velocity-dependent curl fields to the hand. For one group of subjects the manipulandum was fitted with two different handles, one for each force field. No attenuation in interference was observed in these subjects relative to controls who used the same handle for both force fields. CONCLUSIONS/SIGNIFICANCE: These results suggest that in the context of the present learning paradigm, haptic cues on their own are not sufficient to reduce interference and promote learning multiple force fields.

  17. Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations

    DEFF Research Database (Denmark)

    Hemmingsen, Lars Bo Stegeager; Madsen, D.E.; Esbensen, A.L.

    2004-01-01

    A quantitative evaluation of 20 second-generation carbohydrate force fields was carried out using ab initio and density functional methods. Geometry-optimized structures (B3LYP/6-31G(d)) and relative energies using augmented correlation consistent basis sets were calculated in gas phase...... for monosaccharide carbohydrate benchmark systems. Selected results are: (i) The interaction energy of the alpha-D-alucopyranose-H2O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error......-generation carbohydrate force fields. No single force field is consistently better than the others for all the test cases. A statistical assessment of the performance of the force fields indicates that CHEAT(95), CFF, certain versions of Amber and of MM3 have the best overall performance, for these gas phase...

  18. CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands

    Science.gov (United States)

    Mottin, Melina; Souza, Paulo C. T.; Ricci, Clarisse G.; Skaf, Munir S.

    2016-01-01

    The peroxisome proliferator-activated receptor γ (PPARγ) ligands are important therapeutic drugs for the treatment of type 2 diabetes, obesity and cardiovascular diseases. In particular, partial agonists and non-agonists are interesting targets to reduce glucose levels, presenting few side effects in comparison to full agonists. In this work, we present a set of CHARMM-based parameters of a molecular mechanics force field for two PPARγ ligands, GQ16 and SR1664. GQ16 belongs to the thiazolidinedione class of drugs and it is a PPARγ partial agonist that has been shown to promote the “browning” of white adipose tissue. SR1664 is the precursor of the PPARγ non-agonist class of ligands that activates PPARγ in a non-classical manner. Here, we use quantum chemical calculations consistent with the CHARMM protocol to obtain bonded and non-bonded parameters, including partial atomic charges and effective torsion potentials for both molecules. The newly parameterized models were evaluated by examining the behavior of GQ16 and SR1664 free in water and bound to the ligand binding pocket of PPARγ using molecular dynamics simulations. The potential parameters derived here are readily transferable to a variety of pharmaceutical compounds and similar PPARγ ligands. PMID:28025495

  19. Transferable force-field for modelling of CO2, N2, O2 and Ar in all silica and Na+ exchanged zeolites

    Science.gov (United States)

    Vujić, Bojan; Lyubartsev, Alexander P.

    2016-05-01

    In this work we propose a new force field for modelling of adsorption of CO2, N2, O2 and Ar in all silica and Na+ exchanged Si-Al zeolites. The force field has a standard molecular-mechanical functional form with electrostatic and Lennard-Jones interactions satisfying Lorentz-Berthelot mixing rules and thus has a potential for further extension in terms of new molecular types. The parameters for the zeolite framework atom types are optimized by an iterative procedure minimizing the difference with experimental adsorption data for a number of different zeolite structures and Si:Al ratios. The new force field shows a good agreement with available experimental data including those not used in the optimization procedure, and which also shows a reasonable transferability within different zeolite topologies. We suggest a potential usage in screening of different zeolite structures for carbon capture and storage process, and more generally, for separation of other gases.

  20. Force Field Parametrization of Colloidal CdSe Nanocrystals Using an Adaptive Rate Monte Carlo Optimization Algorithm.

    Science.gov (United States)

    Cosseddu, Salvatore; Infante, Ivan

    2017-01-10

    In a typical colloidal CdSe nanocrystal more than 50% of the atoms are located at the surface. These atoms can give rise to electronic traps that can deteriorate the performance of optoelectronic devices made of these nanomaterials. A key challenge in this field is thus to understand with atomistic detail the chemical processes occurring at the nanocrystal surface. Molecular dynamics simulations represent an important tool to unveil these processes, but its implementation is strongly limited by the difficulties of finely tuning classical force fields parameters, primarily caused by the unavailability of experimental data of these materials that are suitable in the parametrization procedures. In this work, we present a general scheme to produce force field parameters from first-principles calculations. This approach is based on a newly developed stochastic optimization algorithm called Adaptive Rate Monte Carlo, which is designed to be robust, accurate, easy-to-use, and flexible enough to be straightforwardly extended to other nanomaterials. We demonstrate that our algorithm provides a set of parameters capable of satisfactorily describing nonstoichiometric CdSe nanocrystals passivated with oleate ligands akin to experimental conditions. We also demonstrate that our new parameters are robust enough to be transferable among crystal structures and nanocrystals of increasing sizes up to the bulk.

  1. Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes.

    Science.gov (United States)

    Liu, Cui; Li, Yue; Han, Bing-Yu; Gong, Li-Dong; Lu, Li-Nan; Yang, Zhong-Zhi; Zhao, Dong-Xia

    2017-05-09

    DNA damage caused by oxidized bases can lead to aging and cancer in living beings. Luckily, a repair enzyme is able to repair the oxidized bases. The key step is to accurately recognize the oxidized bases, which mainly rely on complex hydrogen bond interactions. We have calibrated the charge parameters and torsional parameters of the ABEEMσπ polarization force field (ABEEMσπ PFF) to accurately describe the intermolecular and intramolecular interactions. Taking the experiment and quantum chemical method as the benchmark, a series of properties of base pair-amino acid residue systems, DNA and DNA-protein interaction systems were calculated and compared with those of other force fields. We have done a tremendous amount of tasks in testing, calibrations, and analyses. The ABEEMσπ PFF not only explicitly gives the position and the partial charge of lone-pair electrons but also introduces a function kHB to fit special electrostatic interactions in hydrogen bond interaction regions. Therefore, it can accurately simulate the polarization effect and charge transfer of hydrogen bond interactions, especially for charged systems and sulfur-containing systems, such as the binding energy between amino acid and base pairs (24-28 kcal/mol), which is induced by charge transfer. The RMSD of ABEEMσπ PFF is 1.18 kcal/mol, whereas the RMSD of Amber OL15 is 8.21 kcal/mol. The relative positions of the amino acid residue have significantly changed, and the hydrogen bonds were broken when simulated by fixed charge force fields. In addition, owing to refitting the reasonable torsional parameters, the geometric structures optimized by ABEEMσπ PFF were well consistent with those of the M06-2X/6-311++G** method, but the simulations by fixed force fields have a large rotation of methyl and distortion of the plane of the base pair. After extensive MD simulation with four test DNAs and a DNA-protein system, we conclude that ABEEMσπ PFF shows better agreement when compared to

  2. Application of the linear/exponential hybrid force field scaling scheme to the bond length alternation modes of polyacetylene

    Science.gov (United States)

    Yang, Shujiang; Kertesz, Miklos

    2006-12-01

    The two bond length alternation related backbone carbon-carbon stretching Raman active normal modes of polyacetylene are notoriously difficulty to predict theoretically. We apply our new linear/exponential scaled quantum mechanical force field scheme to tackle this problem by exponentially adjusting the decay of the coupling force constants between backbone stretchings based on their distance which extends over many neighbors. With transferable scaling parameters optimized by least squares fitting to the experimental vibrational frequencies of short oligoenes, the scaled frequencies of trans-polyacetylene and its isotopic analogs agree very well with experiments. The linear/exponential scaling scheme is also applicable to the cis-polyacetylene case.

  3. Free Energy-Based Coarse-Grained Force Field for Binary Mixtures of Hydrocarbons, Nitrogen, Oxygen, and Carbon Dioxide.

    Science.gov (United States)

    Cao, Fenglei; Deetz, Joshua D; Sun, Huai

    2017-01-23

    The free energy based Lennard-Jones 12-6 (FE-12-6) coarse-grained (CG) force field developed for alkanes1 has been extended to model small molecules of light hydrocarbons (methane, ethane, propane, butane, and isobutane), nitrogen, oxygen, and carbon dioxide. The adjustable parameters of the FE-12-6 potential are determined by fitting against experimental vapor-liquid equilibrium (VLE) curves and heat of vaporization (HOV) data for pure substance liquids. Simulations using the optimized FE-12-6 parameters correctly reproduced experimental measures of the VLE, HOV, density, vapor pressure, compressibility, critical point, and surface tension for pure substances over a wide range of thermodynamic states. The force field parameters optimized for pure substances were tested on methane/butane, nitrogen/decane, and carbon dioxide/decane binary mixtures to predict their vapor-liquid equilibrium phase diagrams. It is found that for nonpolar molecules represented by different sized beads, a common scaling factor (0.08) that reduces the strength of the interaction potential between unlike beads, generated using Lorentz-Berthelot (LB) combination rules, is required to predict vapor-liquid phase equilibria accurately.

  4. Development of a transferable reactive force field for cobalt.

    Science.gov (United States)

    Labrosse, Matthew R; Johnson, J Karl; van Duin, Adri C T

    2010-05-13

    ReaxFF provides a method to describe bond-breaking and bond-forming events that can be applied to large-scale molecular dynamics simulations. This article describes the development of a ReaxFF potential for cobalt. This potential is transferable to a wide variety of cobalt systems, including various crystal structures, surfaces, clusters, and defects. The potential parameters were obtained from an extensive set of ab initio calculations. We have tested these parameters against additional DFT calculations not included in the fitting data set and found that ReaxFF provides similar or superior agreement with the DFT results compared to accepted embedded atom method descriptions for Co. We validated this potential by performing large-scale molecular dynamics simulations to predict the melting point, diffusion coefficients for the liquid as a function of temperature, and vacancy-mediated diffusion coefficients in the solid as a function of temperature and vacancy concentration. Results are compared with other theoretical methods and experiments where available. Since the ReaxFF method allows straightforward extensions to alloys and heterogeneous materials, including first-row elements, the ReaxFF parameters described here provide a foundation for the simulation of a wide range of Co-containing materials.

  5. Force-Field Prediction of Materials Properties in Metal-Organic Frameworks

    Science.gov (United States)

    2016-01-01

    In this work, MOF bulk properties are evaluated and compared using several force fields on several well-studied MOFs, including IRMOF-1 (MOF-5), IRMOF-10, HKUST-1, and UiO-66. It is found that, surprisingly, UFF and DREIDING provide good values for the bulk modulus and linear thermal expansion coefficients for these materials, excluding those that they are not parametrized for. Force fields developed specifically for MOFs including UFF4MOF, BTW-FF, and the DWES force field are also found to provide accurate values for these materials’ properties. While we find that each force field offers a moderately good picture of these properties, noticeable deviations can be observed when looking at properties sensitive to framework vibrational modes. This observation is more pronounced upon the introduction of framework charges. PMID:28008758

  6. The Rotational Spectrum and Anharmonic Force Field of Chlorine Dioxide, OClO

    Science.gov (United States)

    Muller, Holger S. P.; Sorensen, G.; Birk, Manfred; Friedl, Randy R.

    1997-01-01

    The ground state rotational and quartic centrifugal distortion constants, their vibrational changes, and the sextic centrifugal distortion constants were used in a calculation of the quartic force field together with data from infrared studies.

  7. A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

    Directory of Open Access Journals (Sweden)

    James P. Ewen

    2016-08-01

    Full Text Available For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i accurately predict important properties of long-chain, linear molecules; and (ii reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP, allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-tom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are

  8. Adaptation of multi-joint balance coordination to whole body force fields

    OpenAIRE

    Engelhart, Denise; Schouten, Alfred; Aarts, Ronald; Pasma, J.; Meskers, Carel; Maier, Andrea; Kooij, van der, Marieke

    2014-01-01

    Background and aim: The ankles and the hips play an important role in standing balance. Multi-joint coordination adapts with task, the magnitude and type of disturbance [1]. Arm studies show that postural responses are highly dependent on externally applied force fields [2]. Our aim is to study how multi-joint postural responses in standing depend on such force fields, using closed loop system identification techniques (CLSIT) where two disturbances are applied [3]. This offers knowledge abou...

  9. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

    Science.gov (United States)

    Maisuradze, Gia G; Senet, Patrick; Czaplewski, Cezary; Liwo, Adam; Scheraga, Harold A

    2010-04-08

    Coarse-grained molecular dynamics simulations offer a dramatic extension of the time-scale of simulations compared to all-atom approaches. In this article, we describe the use of the physics-based united-residue (UNRES) force field, developed in our laboratory, in protein-structure simulations. We demonstrate that this force field offers about a 4000-times extension of the simulation time scale; this feature arises both from averaging out the fast-moving degrees of freedom and reduction of the cost of energy and force calculations compared to all-atom approaches with explicit solvent. With massively parallel computers, microsecond folding simulation times of proteins containing about 1000 residues can be obtained in days. A straightforward application of canonical UNRES/MD simulations, demonstrated with the example of the N-terminal part of the B-domain of staphylococcal protein A (PDB code: 1BDD, a three-alpha-helix bundle), discerns the folding mechanism and determines kinetic parameters by parallel simulations of several hundred or more trajectories. Use of generalized-ensemble techniques, of which the multiplexed replica exchange method proved to be the most effective, enables us to compute thermodynamics of folding and carry out fully physics-based prediction of protein structure, in which the predicted structure is determined as a mean over the most populated ensemble below the folding-transition temperature. By using principal component analysis of the UNRES folding trajectories of the formin-binding protein WW domain (PDB code: 1E0L; a three-stranded antiparallel beta-sheet) and 1BDD, we identified representative structures along the folding pathways and demonstrated that only a few (low-indexed) principal components can capture the main structural features of a protein-folding trajectory; the potentials of mean force calculated along these essential modes exhibit multiple minima, as opposed to those along the remaining modes that are unimodal. In addition

  10. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization

    Energy Technology Data Exchange (ETDEWEB)

    Mazack, Michael J. M., E-mail: mazack@mazack.org [Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431 (United States); Gao, Jiali, E-mail: gao@jialigao.org [Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455-0431 (United States); State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun, Jilin Province 130028 (China)

    2014-05-28

    The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

  11. Heterogeneous Memorized Continuous Time Random Walks in an External Force Fields

    Science.gov (United States)

    Wang, Jun; Zhou, Ji; Lv, Long-Jin; Qiu, Wei-Yuan; Ren, Fu-Yao

    2014-09-01

    In this paper, we study the anomalous diffusion of a particle in an external force field whose motion is governed by nonrenewal continuous time random walks with correlated memorized waiting times, which involves Reimann-Liouville fractional derivative or Reimann-Liouville fractional integral. We show that the mean squared displacement of the test particle which is dependent on its location of the form (El-Wakil and Zahran, Chaos Solitons Fractals, 12, 1929-1935, 2001) where is the anomalous exponent, the diffusion exponent is dependent on the model parameters. We obtain the Fokker-Planck-type dynamic equations, and their stationary solutions are of the Boltzmann-Gibbs form. These processes obey a generalized Einstein-Stokes-Smoluchowski relation and the second Einstein relation. We observe that the asymptotic behavior of waiting times and subordinations are of stretched Gaussian distributions. We also discuss the time averaged in the case of an harmonic potential, and show that the process exhibits aging and ergodicity breaking.

  12. Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields

    Science.gov (United States)

    Rudzinski, J. F.; Bereau, T.

    2016-10-01

    The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG representation usually results in faster, albeit inconsistent, dynamics. In this work, we rely on Markov state models to simultaneously characterize the static and kinetic properties of two CG peptide force fields—one top-down and one bottom-up. Instead of a rigorous evolution of CG dynamics (e.g., using a generalized Langevin equation), we attempt to improve the description of kinetics by simply altering the existing CG models, which employ standard Langevin dynamics. By varying masses and relevant force-field parameters, we can improve the timescale separation of the slow kinetic processes, achieve a more consistent ratio of mean-first-passage times between metastable states, and refine the relative free-energies between these states. Importantly, we show that the incorporation of kinetic information into a structure-based parametrization improves the description of the helix-coil transition sampled by a minimal CG model. While structure-based models understabilize the helical state, kinetic constraints help identify CG models that improve the ratio of forward/backward timescales by effectively hindering the sampling of spurious conformational intermediate states.

  13. An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field.

    Science.gov (United States)

    Xiang, Jin Yu; Ponder, Jay W

    2014-01-01

    An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies.

  14. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    Science.gov (United States)

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  15. First principles derived, transferable force fields for CO2 adsorption in Na-exchanged cationic zeolites.

    Science.gov (United States)

    Fang, Hanjun; Kamakoti, Preeti; Ravikovitch, Peter I; Aronson, Matthew; Paur, Charanjit; Sholl, David S

    2013-08-21

    The development of accurate force fields is vital for predicting adsorption in porous materials. Previously, we introduced a first principles-based transferable force field for CO2 adsorption in siliceous zeolites (Fang et al., J. Phys. Chem. C, 2012, 116, 10692). In this study, we extend our approach to CO2 adsorption in cationic zeolites which possess more complex structures. Na-exchanged zeolites are chosen for demonstrating the approach. These methods account for several structural complexities including Al distribution, cation positions and cation mobility, all of which are important for predicting adsorption. The simulation results are validated with high-resolution experimental measurements of isotherms and microcalorimetric heats of adsorption on well-characterized materials. The choice of first-principles method has a significant influence on the ability of force fields to accurately describe CO2-zeolite interactions. The PBE-D2 derived force field, which performed well for CO2 adsorption in siliceous zeolites, does not do so for Na-exchanged zeolites; the PBE-D2 method overestimates CO2 adsorption energies on multi-cation sites that are common in cationic zeolites with low Si/Al ratios. In contrast, a force field derived from the DFT/CC method performed well. Agreement was obtained between simulation and experiment not only for LTA-4A on which the force field fitting is based, but for other two common adsorbents, NaX and NaY.

  16. A transferable force field for CdS-CdSe-PbS-PbSe solid systems.

    Science.gov (United States)

    Fan, Zhaochuan; Koster, Rik S; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O; Tichelaar, Frans D; Zandbergen, Henny W; van Huis, Marijn A; Vlugt, Thijs J H

    2014-12-28

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

  17. Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    Science.gov (United States)

    KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

    2014-01-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

  18. Theoretical Investigation of Hydrogen Adsorption and Dissociation on Iron and Iron Carbide Surfaces Using the ReaxFF Reactive Force Field Method

    Energy Technology Data Exchange (ETDEWEB)

    Zou, Chenyu; van Duin, Adri C.T.; Sorescu, Dan C.

    2012-06-01

    We have developed a ReaxFF reactive force field to describe hydrogen adsorption and dissociation on iron and iron carbide surfaces relevant for simulation of Fischer–Tropsch (FT) synthesis on iron catalysts. This force field enables large system (>>1000 atoms) simulations of hydrogen related reactions with iron. The ReaxFF force field parameters are trained against a substantial amount of structural and energetic data including the equations of state and heats of formation of iron and iron carbide related materials, as well as hydrogen interaction with iron surfaces and different phases of bulk iron. We have validated the accuracy and applicability of ReaxFF force field by carrying out molecular dynamics simulations of hydrogen adsorption, dissociation and recombination on iron and iron carbide surfaces. The barriers and reaction energies for molecular dissociation on these two types of surfaces have been compared and the effect of subsurface carbon on hydrogen interaction with iron surface is evaluated. We found that existence of carbon atoms at subsurface iron sites tends to increase the hydrogen dissociation energy barrier on the surface, and also makes the corresponding hydrogen dissociative state relatively more stable compared to that on bare iron. These properties of iron carbide will affect the dissociation rate of H{sub 2} and will retain more surface hydride species, thus influencing the dynamics of the FT synthesis process.

  19. Toward optimized potential functions for protein-protein interactions in aqueous solutions: osmotic second virial coefficient calculations using the MARTINI coarse-grained force field.

    Science.gov (United States)

    Stark, Austin C; Andrews, Casey T; Elcock, Adrian H

    2013-09-10

    Coarse-grained (CG) simulation methods are now widely used to model the structure and dynamics of large biomolecular systems. One important issue for using such methods - especially with regard to using them to model, for example, intracellular environments - is to demonstrate that they can reproduce experimental data on the thermodynamics of protein-protein interactions in aqueous solutions. To examine this issue, we describe here simulations performed using the popular coarse-grained MARTINI force field, aimed at computing the thermodynamics of lysozyme and chymotrypsinogen self-interactions in aqueous solution. Using molecular dynamics simulations to compute potentials of mean force between a pair of protein molecules, we show that the original parameterization of the MARTINI force field is likely to significantly overestimate the strength of protein-protein interactions to the extent that the computed osmotic second virial coefficients are orders of magnitude more negative than experimental estimates. We then show that a simple down-scaling of the van der Waals parameters that describe the interactions between protein pseudo-atoms can bring the simulated thermodynamics into much closer agreement with experiment. Overall, the work shows that it is feasible to test explicit-solvent CG force fields directly against thermodynamic data for proteins in aqueous solutions, and highlights the potential usefulness of osmotic second virial coefficient measurements for fully parameterizing such force fields.

  20. Quartic canonical force field in curvilinear internal coordinates for XY3 (D3h) molecules. The case of the BH3 molecule.

    Science.gov (United States)

    Ródenas, Consuelo Rosales; Quesada, Juana Vázquez; Torres, Emilio Martínez; González, Juan Jesús López

    2014-06-01

    Using the canonical force field theory, expressions of quadratic, cubic, and quartic canonical force constants are obtained for XY3 (D3h) molecules in curvilinear redundant coordinates, i.e., simple valence internal coordinates (VICs), in terms of force constants in normal coordinates and in independent symmetry coordinates. To carry out this task, it was previously necessary to obtain for the first time the non-linear redundancy relation and the corresponding orthogonal projection onto the pure vibrational manifold for XY3 (D3h) molecules corresponding to a set of seven VICs. As an application, the quartic canonical force field in curvilinear redundant internal coordinates of BH3 is determined from ab initio force fields in normal coordinates calculated at the coupled-cluster singles and doubles level with perturbative treatment of the triples in conjunction with a triple- and quadruple-ζ size basis set. This anharmonic force field so obtained for the borane molecule, and in general for XY3 (D3h) molecules, is uniquely defined (therefore in an unambiguous form) and depending on the same number of parameters, i.e., force constants, when independent coordinates (natural or symmetry) are used in its description.

  1. Task-space separation principle: a force-field approach to motion planning for redundant manipulators.

    Science.gov (United States)

    Tommasino, Paolo; Campolo, Domenico

    2017-02-03

    In this work, we address human-like motor planning in redundant manipulators. Specifically, we want to capture postural synergies such as Donders' law, experimentally observed in humans during kinematically redundant tasks, and infer a minimal set of parameters to implement similar postural synergies in a kinematic model. For the model itself, although the focus of this paper is to solve redundancy by implementing postural strategies derived from experimental data, we also want to ensure that such postural control strategies do not interfere with other possible forms of motion control (in the task-space), i.e. solving the posture/movement problem. The redundancy problem is framed as a constrained optimization problem, traditionally solved via the method of Lagrange multipliers. The posture/movement problem can be tackled via the separation principle which, derived from experimental evidence, posits that the brain processes static torques (i.e. posture-dependent, such as gravitational torques) separately from dynamic torques (i.e. velocity-dependent). The separation principle has traditionally been applied at a joint torque level. Our main contribution is to apply the separation principle to Lagrange multipliers, which act as task-space force fields, leading to a task-space separation principle. In this way, we can separate postural control (implementing Donders' law) from various types of tasks-space movement planners. As an example, the proposed framework is applied to the (redundant) task of pointing with the human wrist. Nonlinear inverse optimization (NIO) is used to fit the model parameters and to capture motor strategies displayed by six human subjects during pointing tasks. The novelty of our NIO approach is that (i) the fitted motor strategy, rather than raw data, is used to filter and down-sample human behaviours; (ii) our framework is used to efficiently simulate model behaviour iteratively, until it converges towards the experimental human strategies.

  2. Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field.

    Science.gov (United States)

    Miguel, Virginia; Perillo, Maria A; Villarreal, Marcos A

    2016-11-01

    Coarse-grained (CG) models allow enlarging the size and time scales that are reachable by atomistic molecular dynamics simulations. A CG force field (FF) for lipids and amino acids that possesses a polarizable water model has been developed following the MARTINI parametrization strategy, the BMW-MARTINI [1]. We tested the BMW-MARTINI FF capability to describe some structural and thermodynamical properties of lipid monolayers and bilayers. We found that, since the surface tension values of oil/water interfaces calculated with the model are not correct, compression isotherms of lipid monolayers present artifacts. Also, this FF predicts DPPC and DAPC bilayers to remain in the Lα phase at temperatures as low as 283K, contrary to the expected from their experimental Tm values. Finally, simulations at constant temperature of bilayers of saturated lipids belonging to PC homologous, showed an increase in the mean molecular area (Mma) upon increasing the chain length, inversely to the experimental observation. We refined BMW-MARTINI FF by modifying as few parameters as possible in order to bring simulated and experimental measurements closer. We have also modified structural parameters of the lipid geometry that do not have direct influence in global properties of the bilayer membranes or monolayers, but serve to approach the obtained CG geometry to atomistic reference values. The refined FF is able to better reproduce phase transition temperatures and Mma for saturated PC bilayers than BMW-MARTINI and MARTINI FF. Finally, the simulated surface pressure-Mma isotherms of PC monolayers resemble the experimental ones and eliminate serious artifacts of previous models.

  3. The SPASIBA Force Field for Studying Iron-Tannins Interactions : Application to Fe3+ /Fe2+ Catechol Complexe

    Directory of Open Access Journals (Sweden)

    G. Vergoten

    2007-03-01

    Full Text Available The SPASIBA force field parameters have been obtained for Fe3+ /Fe2+ -Oxygeninteractions occuring between non-heminic iron and hydroxyl groups of polyphenols foundin tannins. These parameters were derived from normal modes analyses based on quantumchemical calculations using the Density Functional Theory (DFT. Four models involvingcomplexation of iron with water ([Fe(H2O6]3+ , [Fe(H2O6]2+ and with cathechol molecules([Fe(cat2(H2O2]-1, [Fe(cat2(H2O2]-2 were studied using the Density Functional Theoryand the B3LYP hybrid functional under high spin states of iron.

  4. Ionic force field optimization based on single-ion and ion-pair solvation properties

    CERN Document Server

    Fyta, Maria; Dzubiella, Joachim; Vrbka, Lubos; Netz, Roland R

    2009-01-01

    Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional $\\{\\sigma,\\e...

  5. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields.

    Science.gov (United States)

    Götz, Andreas W; Bucher, Denis; Lindert, Steffen; McCammon, J Andrew

    2014-04-08

    The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.

  6. Transferability of different classical force fields for right and left handed α-helices constructed from enantiomeric amino acids.

    Science.gov (United States)

    Biswas, Santu; Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip

    2016-02-21

    Amino acids can form d and l enantiomers, of which the l enantiomer is abundant in nature. The naturally occurring l enantiomer has a greater preference for a right handed helical conformation, and the d enantiomer for a left handed helical conformation. The other conformations, that is, left handed helical conformations of the l enantiomers and right handed helical conformations of the d enantiomers, are not common. The energetic differences between left and right handed alpha helical peptide chains constructed from enantiomeric amino acids are investigated using quantum chemical calculations (using the M06/6-311g(d,p) level of theory). Further, the performances of commonly used biomolecular force fields (OPLS/AA, CHARMM27/CMAP and AMBER) to represent the different helical conformations (left and right handed) constructed from enantiomeric (D and L) amino acids are evaluated. 5- and 10-mer chains from d and l enantiomers of alanine, leucine, lysine, and glutamic acid, in right and left handed helical conformations, are considered in the study. Thus, in total, 32 α-helical polypeptides (4 amino acids × 4 conformations of 5-mer and 10-mer) are studied. Conclusions, with regards to the performance of the force fields, are derived keeping the quantum optimized geometry as the benchmark, and on the basis of phi and psi angle calculations, hydrogen bond analysis, and different long range helical order parameters.

  7. An extended version of Boyd's force field method applicable to heteroatomic molecules. Part 1. Adenine and uracil

    Science.gov (United States)

    Espinosa-Müller, A. W.; Bravo, A. N.

    The force field method developed by Boyd is extended to include molecules containing atoms other than C and H (e.g., N, O, P, S, Cl, Br,…). A new set of force field parameters is determined in order to redefine the potential energy functions that govern the dynamics of the internal (valence coordinates) degrees of freedom of a molecule. It is shown that the minimum of the partial potential energy surface is significantly affected by electrostatic intramolecular interactions. In this regard the non-bonded interactions appears to be less important than the dipole-dipole type interactions for a given interatomic distance when heteroatoms are present in the molecular framework. The reliability of the extended method as regards minimized structure, vibrational spectra and thermodynamic properties has been checked for more than 20 polyatomic molecules. From the correlation between calculated and experimental properties it is concluded that the method has good potential for further applications on polyatomic molecules with increasing size and topological compexities such as adenine and uracil.

  8. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    Science.gov (United States)

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-05

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc.

  9. Non-Markovian Brownian motion in a magnetic field and time-dependent force fields

    Science.gov (United States)

    Hidalgo-Gonzalez, J. C.; Jiménez-Aquino, J. I.; Romero-Bastida, M.

    2016-11-01

    This work focuses on the derivation of the velocity and phase-space generalized Fokker-Planck equations for a Brownian charged particle embedded in a memory thermal bath and under the action of force fields: a constant magnetic field and arbitrary time-dependent force fields. To achieve the aforementioned goal we use a Gaussian but non-Markovian generalized Langevin equation with an arbitrary friction memory kernel. In a similar way, the generalized diffusion equation in the zero inertia limit is also derived. Additionally we show, in the absence of the time-dependent external forces, that, if the fluctuation-dissipation relation of the second kind is valid, then the generalized Langevin dynamics associated with the charged particle reaches a stationary state in the large-time limit. The consistency of our theoretical results is also verified when they are compared with those derived in the absence of the force fields and in the Markovian case.

  10. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  11. The electromagnetic force field, fluid flow field and temperature profiles in levitated metal droplets

    Science.gov (United States)

    El-Kaddah, N.; Szekely, J.

    1982-01-01

    A mathematical representation was developed for the electromagnetic force field, the flow field, the temperature field (and for transport controlled kinetics), in a levitation melted metal droplet. The technique of mutual inductances was employed for the calculation of the electromagnetic force field, while the turbulent Navier - Stokes equations and the turbulent convective transport equations were used to represent the fluid flow field, the temperature field and the concentration field. The governing differential equations, written in spherical coordinates, were solved numerically. The computed results were in good agreement with measurements, regarding the lifting force, and the average temperature of the specimen and carburization rates, which were transport controlled.

  12. Prediction of adsorption of small molecules in porous materials based on ab initio force field method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Computational prediction of adsorption of small molecules in porous materials has great impact on the basic and applied research in chemical engineering and material sciences. In this work,we report an approach based on grand canonical ensemble Monte Carlo(GCMC) simulations and ab initio force fields. We calculated the adsorption curves of ammonia in ZSM-5 zeolite and hydrogen in MOF-5(a metal-organic-framework material). The predictions agree well with experimental data. Because the predictions are based on the first principle force fields,this approach can be used for the adsorption prediction of new molecules or materials without experimental data as guidance.

  13. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    OpenAIRE

    Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Anil O. Yalcin; Frans D. Tichelaar; Zandbergen, Henny W.; Van Huis, Marijn A.; Vlugt, Thijs J H

    2014-01-01

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and C...

  14. Exploring the properties of valence electron based potential functions for the nonbonded interactions in atomistic force fields

    CERN Document Server

    Plattner, Nuria

    2016-01-01

    The possibility to construct and parametrize the nonbonded interactions in atomistic force fields based on the valence electron structure of molecules is explored in this paper. Three different charge distribution models using simple valence electron based potential functions are introduced and compared. It is shown that the three models can be constructed such that they only require one adjustable parameter for the electrostatic potential of a molecule. The accuracy of the electrostatic potential is evaluated for the three models and compared to population-derived charges and higher order multipole moments for a set of 12 small molecules. Furthermore the accuracy and parametrization of the interaction energies of the three models is evaluated based on {\\it ab initio} intermolecular interaction energies. It is shown that the valence electron potential models provide systematic advantages over conventional point charge models for the calculation of intermolecular interaction energies even with the very simple ...

  15. Development of a Polarizable Force Field for Molecular Dynamics Simulations of Poly (Ethylene Oxide) in Aqueous Solution.

    Science.gov (United States)

    Starovoytov, Oleg N; Borodin, Oleg; Bedrov, Dmitry; Smith, Grant D

    2011-06-14

    We have developed a quantum chemistry-based polarizable potential for poly(ethylene oxide) (PEO) in aqueous solution based on the APPLE&P polarizable ether and the SWM4-DP polarizable water models. Ether-water interactions were parametrized to reproduce the binding energy of water with 1,2-dimethoxyethane (DME) determined from high-level quantum chemistry calculations. Simulations of DME-water and PEO-water solutions at room temperature using the new polarizable potentials yielded thermodynamic properties in good agreement with experimental results. The predicted miscibility of PEO and water as a function of the temperature was found to be strongly correlated with the predicted free energy of solvation of DME. The developed nonbonded force field parameters were found to be transferrable to poly(propylene oxide) (PPO), as confirmed by capturing, at least qualitatively, the miscibility of PPO in water as a function of the molecular weight.

  16. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  17. An Energy Conservative Ray-Tracing Method With a Time Interpolation of the Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Jin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-02-10

    A new algorithm that constructs a continuous force field interpolated in time is proposed for resolving existing difficulties in numerical methods for ray-tracing. This new method has improved accuracy, but with the same degree of algebraic complexity compared to Kaisers method.

  18. Hybrid simulations : combining atomistic and coarse-grained force fields using virtual sites

    NARCIS (Netherlands)

    Rzepiela, Andrzej J.; Louhivuori, Martti; Peter, Christine; Marrink, Siewert J.

    2011-01-01

    Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. I

  19. Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case

    DEFF Research Database (Denmark)

    Rossi, G.; Monticelli, L.; Puisto, S. R.

    2011-01-01

    in the parameterization. We refine the MARTINI procedure by including one additional target property related to the structure of the polymer, namely the radius of gyration. The force-field optimization is mainly based on experimental data. We test our procedure on polystyrene, a standard benchmark for coarse-grained (CG...

  20. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    Science.gov (United States)

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.

  1. Molecular simulation of gas adsorption and diffusion in a breathing MOF using a rigid force field.

    Science.gov (United States)

    García-Pérez, E; Serra-Crespo, P; Hamad, S; Kapteijn, F; Gascon, J

    2014-08-14

    Simulation of gas adsorption in flexible porous materials is still limited by the slow progress in the development of flexible force fields. Moreover, the high computational cost of such flexible force fields may be a drawback even when they are fully developed. In this work, molecular simulations of gas adsorption and diffusion of carbon dioxide and methane in NH2-MIL-53(Al) are carried out using a linear combination of two crystallographic structures with rigid force fields. Once the interactions of carbon dioxide molecules and the bridging hydroxyls groups of the framework are optimized, an excellent match is found for simulations and experimental data for the adsorption of methane and carbon dioxide, including the stepwise uptake due to the breathing effect. In addition, diffusivities of pure components are calculated. The pore expansion by the breathing effect influences the self-diffusion mechanism and much higher diffusivities are observed at relatively high adsorbate loadings. This work demonstrates that using a rigid force field combined with a minimum number of experiments, reproduces adsorption and simulates diffusion of carbon dioxide and methane in the flexible metal-organic framework NH2-MIL-53(Al).

  2. An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates.

    Science.gov (United States)

    Sibaev, M; Crittenden, D L

    2016-06-01

    In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm(-1) in fundamental frequencies, on average, across a sizable test set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/.

  3. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

    CERN Document Server

    Kührová, Petra; Bottaro, Sandro; Bussi, Giovanni; Šponer, Jiří; Otyepka, Michal; Banáš, Pavel

    2016-01-01

    The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that ...

  4. Zeolite force fields and experimental siliceous frameworks in a comparative infrared study

    NARCIS (Netherlands)

    Bueno-Perez, R.; Calero, S.; Dubbeldam, D.; Ania, C.O.; Parra, J.B.; Zaderenko, A.P.; Merkling, P.J.

    2012-01-01

    Infrared spectra (IR) of a great variety of zeolite frameworks in the limit of pure silica composition are calculated by molecular dynamics and also recorded experimentally. This enables us to study and assess the effect of three flexible force fields from the literature developed for zeolites in

  5. Adaptation of multi-joint balance coordination to whole body force fields

    NARCIS (Netherlands)

    Engelhart, Denise; Schouten, Alfred; Aarts, Ronald; Pasma, J.; Meskers, Carel; Maier, Andrea; Kooij, van der Herman

    2014-01-01

    Background and aim: The ankles and the hips play an important role in standing balance. Multi-joint coordination adapts with task, the magnitude and type of disturbance [1]. Arm studies show that postural responses are highly dependent on externally applied force fields [2]. Our aim is to study how

  6. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    NARCIS (Netherlands)

    Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.

    2014-01-01

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heterona

  7. Coarse-graining poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) block copolymers using the MARTINI force field.

    Science.gov (United States)

    Nawaz, Selina; Carbone, Paola

    2014-02-13

    The MARTINI coarse-grain (CG) force field is extended for a class of triblock block copolymers known as Pluronics. Existing MARTINI bead types are used to model the non-bonded part of the potential while single chain properties for both homopolymers, poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), are used to develop the bonded interactions. The new set of force field parameters reproduces structural and dynamical properties of high molecular weight homo- and copolymers. The CG model is moderately transferable in solvents of different polarity and concentration; however, the PEO homopolymer model presents a reduced thermodynamic transferability especially in water probably due to the lack of hydrogen bonds with the solvent. Our simulations of a monolayer of Pluronic L44 show polymer-brush-like characteristics for the PEO segments which protrude into the aqueous phase. Other membrane properties not easily accessible using experimental techniques such as its membrane thickness are also calculated.

  8. Solvent reorganization energies in A-DNA, B-DNA, and rhodamine 6G-DNA complexes from molecular dynamics simulations with a polarizable force field.

    Science.gov (United States)

    Vladimirov, Egor; Ivanova, Anela; Rösch, Notker

    2009-04-02

    We estimate solvent reorganization energies lambda(s) of electron transfer (ET) in DNA stacks between positively charged guanine (acceptor) and neutral guanine (donor), as well as in rhodamine 6G (R6G)-DNA complexes between R6G (acceptor) and neutral guanine (donor) from molecular dynamics simulations that used a polarizable force field in combination with a polarizable water model. We compare results from the polarizable scheme with those from a common nonpolarizable analogue. We also discuss the influence of charge sets, separate contributions of solute and solvent electronic polarizations, and partial contributions of different molecular groups to changes of lambda(s) due to electronic polarization. Independent of donor-acceptor distances, solvent reorganization energies of ET processes in DNA duplexes from a polarizable force field are about 30% smaller than the corresponding results from a nonpolarizable force field. The effective optical dielectric constant epsilon(infinity) = 1.5, extracted from pertinent scaling factors, is also independent of the donor-acceptor separation over a wide range of distances, from 3.4 to 50.0 A. Reorganization energies calculated with the polarizable force field agree satisfactorily with experimental data for DNA duplexes. Comparison of results for A-DNA and B-DNA forms as well as for the conformational alignment of the dye relative to the duplex in R6G-DNA complexes demonstrates that the conformation of a duplex hardly affects lambda(s). Among these DNA-related systems, the effective parameter epsilon(infinity) is remarkably constant over a broad range of donor-acceptor distances.

  9. Investigation of Multiscale Non-equilibrium Flow Dynamics Under External Force Field

    CERN Document Server

    Xiao, Tianbai

    2016-01-01

    The multiple scale non-equilibrium gaseous flow behavior under external force field is investigated. Both theoretical analysis based on the kinetic model equation and numerical study are presented to demonstrate the dynamic effect of external force on the flow evolution, especially on the non-equilibrium heat flux. The current numerical experiment is based on the well-balanced unified gas-kinetic scheme (UGKS), which presents accurate solutions in the whole flow regime from the continuum Navier-Stokes solution to the transition and free molecular ones. The heat conduction in the non-equilibrium regime due to the external forcing term is quantitatively investigated. In the lid-driven cavity flow study, due to the external force field the density distribution inside cavity gets stratified and a multiscale non-equilibrium flow transport appears in a single gas dynamic system. With the increment of external forcing term, the flow topological structure changes dramatically, and the temperature gradient, shearing s...

  10. CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.

    Science.gov (United States)

    Qi, Yifei; Ingólfsson, Helgi I; Cheng, Xi; Lee, Jumin; Marrink, Siewert J; Im, Wonpil

    2015-09-08

    Coarse-grained simulations are widely used to study large biological systems. Nonetheless, building such simulation systems becomes nontrivial, especially when membranes with various lipid types are involved. Taking advantage of the frameworks in all-atom CHARMM-GUI modules, we have developed CHARMM-GUI Martini Maker for building solution, micelle, bilayer, and vesicle systems as well as systems with randomly distributed lipids using the Martini force field. Martini Maker supports 82 lipid types and different flavors of the Martini force field, including polar and nonpolar Martini, Dry Martini, and ElNeDyn (an elastic network model for proteins). The qualities of the systems generated by Martini Maker are validated by simulations of various examples involving proteins and lipids. We expect Martini Maker to be a useful tool for modeling large, complicated biomolecular systems in a user-friendly way.

  11. The force-field derivation and application of explosive/additive interfaces

    Science.gov (United States)

    Long, Yao; Chen, Jun

    2016-10-01

    The inter-molecular force-field across RDX/(paraffin, fluoropolymer) interfaces are derived from first-principles calculated energies under the GGA+vdW functional. Based on the force-field, the polycrystal structures of mixture explosives are obtained, and a set of thermodynamic properties are calculated, including the elastic constants, thermal expansion coefficient, heat capacity, isothermal curve and the Hugoniot curve. The results are in good agreement with the available experiments, and provide a reasonable prediction about the properties of plastic bonded explosives. We find that the thermal expansion coefficient of a multi-component explosive is not only determined by the properties of the components, but is also affected by the thermal stress at the explosive/additive interfaces.

  12. Simulations of room temperature ionic liquids: From polarizable to coarse-grained force fields

    CERN Document Server

    Salanne, Mathieu

    2015-01-01

    Room temperature ionic liquids (RTILs) are solvent with unusual properties, which are difficult to characterize experimentally because of their intrinsic complexity (large number of atoms, strong Coulomb interactions). Molecular simulations have therefore been essential in our understanding of these systems. Depending on the target property and on the necessity to account for fine details of the molecular structure of the ions, a large range of simulation techniques are available. Here I focus on classical molecular dynamics, in which the level of complexity of the simulation, and therefore the computational cost, mostly depends on the force field. Depending on the representation of the ions, these are either classified as all-atom or coarse-grained. In addition, all-atom force fields may account for polarization effects if necessary. The most widely used methods for RTILs are described together with their main achievements and limitations.

  13. The Sensitivity of Simulated Ocean Biogeochemistry to Forcing Fields Derived from NCEP and MERRA Reanalysis Products

    Science.gov (United States)

    Gregg, Watson; Casey, Nancy

    2010-01-01

    Ocean biogeochemistry models are typically forced by atmospheric and oceanic data derived from reanalysis products. For the NASA Ocean Biogeochemistry Model (NOBM) such reanalysis forcing fields include: surface wind stress, sea surface temperature, ice distributions, shortwave radiation, surface wind speeds and surface atmospheric pressure. Additionally, proper computation of ocean irradiance requires reanalysis products of relative humidity and precipitable water (in addition to aerosol and cloud information which is derived from satellite data). The question posed here is, does the choice of reanalysis products make a difference in the representation of ocean biology and biogeochemistry? NOBM was forced by NCEP and MERRA reanalysis products for the period 2002-2009. We find that in 2009 global distributions and abundances of biological variables (total chlorophyll and nutrients) and carbon (dissolved inorganic and organic carbon and surface pCO2) were similar between the two different forcing fields. Global statistical comparisons with satellite and in situ data also showed negligible differences.

  14. On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields.

    Science.gov (United States)

    Antila, Hanne S; Salonen, Emppu

    2015-04-15

    The Thole induced point dipole model is combined with three different point charge fitting methods, Merz-Kollman (MK), charges from electrostatic potentials using a grid (CHELPG), and restrained electrostatic potential (RESP), and two multipole algorithms, distributed multipole analysis (DMA) and Gaussian multipole model (GMM), which can be used to describe the electrostatic potential (ESP) around molecules in molecular mechanics force fields. This is done to study how the different methods perform when intramolecular polarizability contributions are self-consistently removed from the fitting done in the force field parametrization. It is demonstrated that the polarizable versions of the partial charge models provide a good compromise between accuracy and computational efficiency in describing the ESP of small organic molecules undergoing conformational changes. For the point charge models, the inclusion of polarizability reduced the the average root mean square error of ESP over the test set by 4-10%.

  15. Empirical corrections to the Amber RNA force field with Target Metadynamics

    CERN Document Server

    Gil-Ley, Alejandro; Bussi, Giovanni

    2016-01-01

    The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the alpha and beta backbone angles on the modulation of ...

  16. Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

    Science.gov (United States)

    2014-01-01

    We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

  17. Transferable Force Field for Metal-Organic Frameworks from First-Principles: BTW-FF.

    Science.gov (United States)

    Bristow, Jessica K; Tiana, Davide; Walsh, Aron

    2014-10-14

    We present an ab-initio derived force field to describe the structural and mechanical properties of metal-organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted.

  18. Understanding the Role of Sodium during Adsorption: A Force Field for Alkanes in Sodium-Exchanged Faujasites.

    NARCIS (Netherlands)

    Calero, S.; Dubbeldam, D.; Krishna, R.; Smit, B.; Vlugt, T.J.H.; Denayer, J.F.M.; Martens, J.A.; Maesen, T.L.M.

    2004-01-01

    We have developed a united atom force field able to accurately describe the adsorption properties of linear alkanes in the sodium form of FAU-type zeolites. This force field successfully reproduces experimental adsorption properties of n-alkanes over a wide range of sodium cation densities,

  19. Understanding the Role of Sodium during Adsorption: A Force Field for Alkanes in Sodium-Exchanged Faujasites.

    NARCIS (Netherlands)

    Calero, S.; Dubbeldam, D.; Krishna, R.; Smit, B.; Vlugt, T.J.H.; Denayer, J.F.M.; Martens, J.A.; Maesen, T.L.M.

    2004-01-01

    We have developed a united atom force field able to accurately describe the adsorption properties of linear alkanes in the sodium form of FAU-type zeolites. This force field successfully reproduces experimental adsorption properties of n-alkanes over a wide range of sodium cation densities, temperat

  20. Reply to ``Comment on Conservative Force Fields in Nonextensive Kinetic Theory"

    OpenAIRE

    Lima, J. A. S.; Bezerra, J. R.; Silva, R.

    2003-01-01

    It is shown that the comment by Costa and Meneses [1] did not point any technical or conceptual flaw in our paper titled ``Conservative Force Fields in Nonextensive Kinetic Theory" (Physica A 316, 289 (2002)). In particular, the application of the nonextensive distribution to the historical problem of the unbounded isothermal atmosphere under constant gravity is theoretically correct. It should be stressed that our solution is somewhat connected with a similar solution to a problem appearing ...

  1. Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields.

    Science.gov (United States)

    Curioni, Alessandro; Mordasini, Tiziana; Andreoni, Wanda

    2004-12-01

    A methodology aimed at improving the accuracy of current docking-scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.

  2. Plastic changes in hand proprioception following force-field motor learning.

    Science.gov (United States)

    Goble, Daniel J; Anguera, Joaquin A

    2010-09-01

    Motor neurophysiologists are placing greater emphasis on sensory feedback processing than ever before. In line with this shift, a recent article by Ostry and colleagues provided timely new evidence that force-field motor learning influences not only motor output, but also proprioceptive sense. In this Neuro Forum, the merits and limitations of Ostry and colleagues are explored in the context of recent work on proprioceptive function, including several recent studies from this journal.

  3. Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study.

    Science.gov (United States)

    Künzel, Daniela; Markert, Thomas; Gross, Axel; Benoit, David M

    2009-10-21

    Host-guest networks formed by ordered organic layers are promising candidates for applications in molecular storage and quantum computing. We have studied 2-dimensionally ordered surface template structures of bis(terpyridine)-derived molecules (BTPs) on graphite using force field and DFT methods and compared the results to recent experimental observations. In order to determine the force field best suited for surface calculations, bond lengths and angles, torsional potentials, adsorption and stacking energies of smaller aromatic molecules were calculated with different force fields (Compass, UFF, Dreiding and CVFF). Density functional perturbation theory calculations were used to study the intermolecular interactions between 3,3'-BTP molecules. Structural properties, adsorption energies and rotational barriers of the 3,3'-BTP surface structure and its host-guest systems with phthalocyanine (PcH(2)) or excess 3,3'-BTP as guest molecules have been addressed. In addition, STM images of oligopyridine and phthalocyanine molecules were simulated based on periodic and local density functional theory calculations.

  4. Vibrational analysis of ferrocyanide complex ion based on density functional force field

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sun Kyung; Lee, Choong Keun; Lee, Nam Soo [Chungbuk National Univ., Cheongju (Korea, Republic of); Lee, Sang Ho [The University of Michigan, Ann Arbor (United States)

    2002-02-01

    Vibrational properties of ferrocyanide complex ion, [Fe(CN){sub 6}]{sup 4-}, have been studied based on the force constants obtained from the density functional calculations at B3LYP/6-31G level by means of the normal mode analysis using new bond angle and linear angle internal coordinates recently developed. Vibrations of ferrocyanide were manipulated by twenty-three symmetry force constants. The angled bending deformations of C-Fe-C, the linear bending deformations of Fe-C{identical_to}N and the stretching vibrations of Fe-C have been quantitatively assigned to the calculated frequencies. The force constants in the internal coordinates employed in the modified Urey-Bradley type potential were evaluated on the density functional force field applied, and better interaction force constants in the internal coordinates have been proposed. The valence force constants in the general quadratic valence force field were also given. The stretch-stretch interaction and stretch-bending interaction constants are not sensitive to the geometrical displacement in the valence force field.

  5. Polarizable Force Fields for CO2 and CH4 Adsorption in M-MOF-74.

    Science.gov (United States)

    Becker, Tim M; Heinen, Jurn; Dubbeldam, David; Lin, Li-Chiang; Vlugt, Thijs J H

    2017-03-02

    The family of M-MOF-74, with M = Co, Cr, Cu, Fe, Mg, Mn, Ni, Ti, V, and Zn, provides opportunities for numerous energy related gas separation applications. The pore structure of M-MOF-74 exhibits a high internal surface area and an exceptionally large adsorption capacity. The chemical environment of the adsorbate molecule in M-MOF-74 can be tuned by exchanging the metal ion incorporated in the structure. To optimize materials for a given separation process, insights into how the choice of the metal ion affects the interaction strength with adsorbate molecules and how to model these interactions are essential. Here, we quantitatively highlight the importance of polarization by comparing the proposed polarizable force field to orbital interaction energies from DFT calculations. Adsorption isotherms and heats of adsorption are computed for CO2, CH4, and their mixtures in M-MOF-74 with all 10 metal ions. The results are compared to experimental data, and to previous simulation results using nonpolarizable force fields derived from quantum mechanics. To the best of our knowledge, the developed polarizable force field is the only one so far trying to cover such a large set of possible metal ions. For the majority of metal ions, our simulations are in good agreement with experiments, demonstrating the effectiveness of our polarizable potential and the transferability of the adopted approach.

  6. Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields

    CERN Document Server

    Leontyev, Igor

    2015-01-01

    Although a great number of computational models of water are available today, the majority of current biological simulations are done with simple models, such as TIP3P and SPC, developed almost thirty years ago and only slightly modified since then. The reason is that the non-polarizable force fields that are mostly used to describe proteins and other biological molecules are incompatible with more sophisticated modern polarizable models of water. The issue is electronic polarizability: in liquid state, in protein, and in vacuum the water molecule is polarized differently, and therefore has different properties; thus the only way to describe all these different media with the same model is to use a polarizable water model. However, to be compatible with the force field of the rest of the system, e.g. a protein, the latter should be polarizable as well. Here we describe a novel model of water that is in effect polarizable, and yet compatible with the standard non-polarizable force fields such as AMBER, CHARMM,...

  7. Force-Field Based Quasi-Chemical Method for Rapid Evaluation of Binary Phase Diagrams.

    Science.gov (United States)

    Sweere, Augustinus J M; Fraaije, Johannes G E M

    2015-11-05

    We present the Pair Configurations to Molecular Activity Coefficients (PAC-MAC) method. The method is based on the pair sampling technique of Blanco (Fan, C. F.; Olafson, B. D.; Blanco, M.; Hsu, S. L. Application of Molecular Simulation to Derive Phase Diagrams of Binary Mixtures. Macromolecules 1992, 25, 3667-3676) with an extension that takes the packing of the molecules into account by a free energy model. The intermolecular energy is calculated using classical force fields. PAC-MAC is able to predict activity coefficients and corresponding vapor-liquid equilibrium diagrams at least 4 orders of magnitude faster than molecular simulations. The accuracy of the PAC-MAC method is tested by comparing the results with experimental data and with the results of the COSMO-SAC model (Lin, S.-T.; Sandler, S. I. A Priori Phase Equilibrium Prediction from a Segment Contribution Solvation Model. Ind. Eng. Chem. Res. 2002, 41, 899-913). PAC-MAC (using the OPLS-aa force field) is shown to be comparable in accuracy to COSMO-SAC, at the considerable advantage that PAC-MAC in principle does not require quantum calculation, provided proper force fields to be available.

  8. Non-polarizable force field of water based on the dielectric constant: TIP4P/ε.

    Science.gov (United States)

    Fuentes-Azcatl, Raúl; Alejandre, José

    2014-02-06

    The static dielectric constant at room temperature and the temperature of maximum density are used as target properties to develop, by molecular dynamics simulations, the TIP4P/ε force field of water. The TIP4P parameters are used as a starting point. The key step, to determine simultaneously both properties, is to perform simulations at 240 K where a molecular dipole moment of minimum density is found. The minimum is shifted to larger values of μ as the distance between the oxygen atom and site M, lOM, decreases. First, the parameters that define the dipole moment are adjusted to reproduce the experimental dielectric constant and then the Lennard-Jones parameters are varied to match the temperature of maximum density. The minimum on density at 240 K allows understanding why reported TIP4P models fail to reproduce the temperature of maximum density, the dielectric constant, or both properties. The new model reproduces some of the thermodynamic and transport anomalies of water. Additionally, the dielectric constant, thermodynamics, and dynamical and structural properties at different temperatures and pressures are in excellent agreement with experimental data. The computational cost of the new model is the same as that of the TIP4P.

  9. The infrared spectra and structure of acetylsalicylic acid (aspirin) and its oxyanion: an ab initio force field treatment

    Science.gov (United States)

    Binev, I. G.; Stamboliyska, B. A.; Binev, Y. I.

    1996-05-01

    The structures of acetylsalicylic acid (aspirin) (I) and its oxyanion (II) have been studied by means of infrared spectra and ab initio 3-21 G force field calculations. The 3100-1100 cm -1 region bands of both the aspirin molecule and its oxyanion have been assigned. The theoretical infrared data for the free aspirin anion are in good agreement with the experimental data for aspirin alkali-metal salts in dimethyl sulfoxide- d6. The theoretical geometrical parameters for the isolated aspirin molecule are close to the literature X-ray diffraction data for its dimer in the solid state, except for those of the carboxy group, which participates directly in hydrogen bond formation. The changes in both the spectral and geometrical parameters, caused by the conversion of the aspirin molecule into the anion, are essential, but they are localized mainly within the carboxy group and the adjacent C-Ph bond. This is also true for the changes in the corresponding bond indices and electronic charges.

  10. Polarizable water model for the coarse-grained MARTINI force field.

    Directory of Open Access Journals (Sweden)

    Semen O Yesylevskyy

    2010-06-01

    Full Text Available Coarse-grained (CG simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.

  11. Reproducing basic pKa values for turkey ovomucoid third domain using a polarizable force field.

    Science.gov (United States)

    Click, Timothy H; Kaminski, George A

    2009-06-04

    We have extended our previous studies of calculating acidity constants for the acidic residues found in the turkey ovomucoid third domain protein (OMTKY3) by determining the relative pKa values for the basic residues (Lys13, Arg21, Lys29, Lys34, His52, and Lys55). A polarizable force field (PFF) was employed. The values of the pKa were found by direct comparison of energies of solvated protonated and deprotonated forms of the protein. Poisson-Boltzmann (PBF) and surface generalized Born (SGB) continuum solvation models represent the hydration, and a nonpolarizable fixed-charge OPLS-AA force field was used for comparison. Our results indicate that (i) the pKa values of the basic residues can be found in close agreement with the experimental values when a PFF is used in conjunction with the PBF solvation model, (ii) it is sufficient to take into the account only the residues which are in close proximity (hydrogen bonded) to the residue in question, and (iii) the PBF solvation model is superior to the SGB solvation model for these pKa calculations. The average error with the PBF/PFF model is only 0.7 pH unit, compared with 2.2 and 6.1 units for the PBF/OPLS and SGB/OPLS, respectively. The maximum deviation of the PBF/PFF results from the experimental values is 1.7 pH units compared with 6.0 pH units for the PBF/OPLS. Moreover, the best results were obtained while using an advanced nonpolar energy calculation scheme. The overall conclusion is that this methodology and force field are suitable for the accurate assessment of pKa shifts for both acidic and basic protein residues.

  12. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Morante, S., E-mail: morante@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Rossi, G.C., E-mail: rossig@roma2.infn.it [Dipartimento di Fisica, Università di Roma, “ Tor Vergata ”, INFN, Sezione di Roma 2, Via della Ricerca Scientifica - 00133 Roma (Italy); Centro Fermi-Museo Storico della Fisica e Centro Studi e Ricerche E. Fermi, Compendio del Viminale, Piazza del Viminale 1, I-00184 Rome (Italy)

    2017-02-15

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg–Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann–Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  13. A novel proof of the DFT formula for the interatomic force field of Molecular Dynamics

    Science.gov (United States)

    Morante, S.; Rossi, G. C.

    2017-02-01

    We give a novel and simple proof of the DFT expression for the interatomic force field that drives the motion of atoms in classical Molecular Dynamics, based on the observation that the ground state electronic energy, seen as a functional of the external potential, is the Legendre transform of the Hohenberg-Kohn functional, which in turn is a functional of the electronic density. We show in this way that the so-called Hellmann-Feynman analytical formula, currently used in numerical simulations, actually provides the exact expression of the interatomic force.

  14. Rapid changes in corticospinal excitability during force field adaptation of human walking

    DEFF Research Database (Denmark)

    Barthélemy, Dorothy; Alain, S; Grey, Michael James

    2012-01-01

    Force field adaptation of locomotor muscle activity is one way of studying the ability of the motor control networks in the brain and spinal cord to adapt in a flexible way to changes in the environment. Here, we investigate whether the corticospinal tract is involved in this adaptation. We...... be explained by changes in background TA EMG activity. These effects seemed specific to walking, as similar changes in TA MEP were not seen when seated subjects were tested during static dorsiflexion. These observations suggest that the corticospinal tract contributes to the adaptation of walking...

  15. Dynamics of ions in a water drop using the AMOEBA polarizable force field

    Science.gov (United States)

    Thaunay, Florian; Ohanessian, Gilles; Clavaguéra, Carine

    2017-03-01

    Various ions carrying a charge from -2 to +3 were confined in a drop of 100 water molecules as a way to model coordination properties inside the cluster and at the interface. The behavior of the ions has been followed by molecular dynamics with the AMOEBA polarizable force field. Multiply charged ions and small singly charged ions are found to lie inside the droplet, while bigger monovalent ions sit near the surface. The results provide a coherent picture of average structural properties as well as residence times for which a general trend is proposed, especially for the anions.

  16. Ionic force field optimization based on single-ion and ion-pair solvation properties: going beyond standard mixing rules.

    Science.gov (United States)

    Fyta, Maria; Netz, Roland R

    2012-03-28

    Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.

  17. Vibrational Study and Force Field of the Citric Acid Dimer Based on the SQM Methodology

    Directory of Open Access Journals (Sweden)

    Laura Cecilia Bichara

    2011-01-01

    Full Text Available We have carried out a structural and vibrational theoretical study for the citric acid dimer. The Density Functional Theory (DFT method with the B3LYP/6-31G∗ and B3LYP/6-311++G∗∗ methods have been used to study its structure and vibrational properties. Then, in order to get a good assignment of the IR and Raman spectra in solid phase of dimer, the best fit possible between the calculated and recorded frequencies was carry out and the force fields were scaled using the Scaled Quantum Mechanic Force Field (SQMFF methodology. An assignment of the observed spectral features is proposed. A band of medium intensity at 1242 cm−1 together with a group of weak bands, previously not assigned to the monomer, was in this case assigned to the dimer. Furthermore, the analysis of the Natural Bond Orbitals (NBOs and the topological properties of electronic charge density by employing Bader's Atoms in Molecules theory (AIM for the dimer were carried out to study the charge transference interactions of the compound.

  18. Point Defects in Carbon Nanotubes: ab initio and Force-Fields Based Simulations

    Science.gov (United States)

    Kroes, Jaap; Pietrucci, Fabio; Curioni, Alessandro; Andreoni, Wanda

    2014-03-01

    We present an extended investigation of point defects in carbon nanotubes (CNTs) and their effects on mechanical and electronic properties. This study is based on large-scale calculations using DFT with exchange and correlation functionals of the GGA - including empirical corrections for van-der-Waals interactions - and of the hybrid type. Additional simulations using classical interatomic potentials allow us to obtain a critical comparison between the outcome of DFT and force-fields. The CNT models adopted have a range of sizes and chiralities. In particular, (i) our simulations of oxygen chemisorption revealed a tendency to clustering and the existence of kinetic traps (epoxides), which explain STS data; (ii) the extension to oxygen isovalent species on CNTs and other graphitic surfaces has suggested a simple predictive model for the chemisorption pattern. Moreover, (iii) our analysis shows an intrinsic difficulty of available force fields to account for the energetics of vacancies and adsorption site preferences. Additional results aiming at characterizing the interaction of nitrogen oxides (NOx) with the CNT surface will also be presented. Work supported by SNSF Nano-Tera.ch and CSCS.

  19. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

    Science.gov (United States)

    Betancourt, Marcos R.; Omovie, Sheyore J.

    2009-05-01

    The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.

  20. Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction

    Directory of Open Access Journals (Sweden)

    Mehmet Z. Baykara

    2012-09-01

    Full Text Available Noncontact atomic force microscopy (NC-AFM is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation.In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.

  1. Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

    CERN Document Server

    Van Vleet, Mary J; Stone, Anthony J; Schmidt, J R

    2016-01-01

    Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones (${A}/{r^{12}}$) or Born-Mayer ($A\\exp(-Br)$) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional for...

  2. New wrinkling substrate assay reveals traction force fields of leader and follower cells undergoing collective migration.

    Science.gov (United States)

    Yokoyama, Sho; Matsui, Tsubasa S; Deguchi, Shinji

    2017-01-22

    Physical forces play crucial roles in coordinating collective migration of epithelial cells, but details of such force-related phenomena remain unclear partly due to the lack of robust methodologies to probe the underlying force fields. Here we develop a method for fabricating silicone substrates that detect cellular traction forces with a high sensitivity. Specifically, a silicone elastomer is exposed to oxygen plasma under heating. Removal of the heat shrinks the substrate so as to reduce its critical buckling strain in a spatially uniform manner. Thus, even small cellular traction forces can be visualized as micro-wrinkles that are reversibly emerged on the substrate in a direction orthogonal to the applied forces. Using this technique, we show that so-called leader cells in MDCK-II cell clusters exert significant magnitudes of traction forces distinct from those of follower cells. We reveal that the direction of traction forces is highly correlated with the long axis of the local, individual cells within clusters. These results suggest that the force fields in collective migration of MDCK-II cells are predominantly determined locally at individual cell scale rather than globally at the whole cell cluster scale. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

    Science.gov (United States)

    Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

    2017-10-01

    Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

  4. Applicability of the SQM force field method to the vibrational spectra of sodium acetate.

    Science.gov (United States)

    Keresztury, Gabor; Istvan, Krisztina; Sundius, Tom

    2005-09-08

    The applicability of the scaled quantum mechanical force field (SQM FF) method to the prediction of the vibrational spectra of a charged molecule has been studied by the example of the acetate ion (CH3CO2-) in sodium acetate for which an efficient empirical valence force field (SVFF) based on observed IR spectra of six isotopomers of sodium acetate is available in the literature. Standard SQM FF calculations done on a free acetate ion at the B3LYP/6-31G level failed to give an acceptable estimation of even the most characteristic features of the observed spectra, which can be exemplified by the gross overestimation of the frequency separation of the nu(a)CO2- and nu(s)CO2- vibrations. In search for a better description, SQM calculations were done for three simple structural models of sodium acetate, testing different QM methods. The results indicate that in addition to taking into account the dielectric field effect of the surrounding medium, incorporation of a Na+ counterion is necessary to achieve a realistic simulation of the IR and Raman spectra. Satisfactory results were obtained with a bidentate Na-acetate complex by the SQM method coupled with a continuum model at the B3LYP/6-31+G level, whereas the use of the Onsager-type spherical cavity model and the polarizable continuum model (PCM) were found preferable over SCI-PCM.

  5. Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.

    Science.gov (United States)

    Zhang, Jin; Tuguldur, Badamkhatan; van der Spoel, David

    2015-06-22

    Quantitative prediction of physical properties of liquids is a longstanding goal of molecular simulation. Here, we evaluate the predictive power of the Generalized Amber Force Field (Wang et al. J. Comput. Chem. 2004, 25, 1157-1174) for the Gibbs energy of solvation of organic molecules in organic solvents using the thermodynamics integration (TI) method. The results are compared to experimental data, to a model based on quantitative structure property relations (QSPR), and to the conductor-like screening models for realistic solvation (COSMO-RS) model. Although the TI calculations yield slightly better correlation to experimental results than the other models, in all fairness we should conclude that the difference between the models is minor since both QSPR and COSMO-RS yield a slightly lower RMSD from that of the experiment (<3.5 kJ/mol). By analyzing which molecules (either as solvents or solutes) are outliers in the TI calculations, we can pinpoint where additional parametrization efforts are needed. For the force field based TI calculations, deviations from the experiment occur in particular when compounds containing nitro or ester groups are solvated into other liquids, suggesting that the interaction between these groups and solvents may be too strong. In the COSMO-RS calculations, outliers mainly occur when compounds containing (in particular aromatic) rings are solvated despite using a ring correction term in the calculations.

  6. Advances in RNA molecular dynamics: a simulator's guide to RNA force fields.

    Science.gov (United States)

    Vangaveti, Sweta; Ranganathan, Srivathsan V; Chen, Alan A

    2017-03-01

    Molecular simulations have become an essential tool for biochemical research. When they work properly, they are able to provide invaluable interpretations of experimental results and ultimately provide novel, experimentally testable predictions. Unfortunately, not all simulation models are created equal, and with inaccurate models it becomes unclear what is a bona fide prediction versus a simulation artifact. RNA models are still in their infancy compared to the many robust protein models that are widely in use, and for that reason the number of RNA force field revisions in recent years has been rapidly increasing. As there is no universally accepted 'best' RNA force field at the current time, RNA simulators must decide which one is most suited to their purposes, cognizant of its essential assumptions and their inherent strengths and weaknesses. Hopefully, armed with a better understanding of what goes inside the simulation 'black box,' RNA biochemists can devise novel experiments and provide crucial thermodynamic and structural data that will guide the development and testing of improved RNA models. WIREs RNA 2017, 8:e1396. doi: 10.1002/wrna.1396 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

  7. Combining a polarizable force-field and a coarse-grained polarizable solvent model. II. Accounting for hydrophobic effects.

    Science.gov (United States)

    Masella, Michel; Borgis, Daniel; Cuniasse, Philippe

    2011-09-01

    A revised and improved version of our efficient polarizable force-field/coarse grained solvent combined approach (Masella, Borgis, and Cuniasse, J. Comput. Chem. 2008, 29, 1707) is described. The polarizable pseudo-particle solvent model represents the macroscopic solvent polarization by induced dipoles placed on mobile pseudo-particles. In this study, we propose a new formulation of the energy term handling the nonelectrostatic interactions among the pseudo-particles. This term is now able to reproduce the energetic and structural response of liquid water due to the presence of a hydrophobic spherical cavity. Accordingly, the parameters of the energy term handling the nonpolar solute/solvent interactions have been refined to reproduce the free-solvation energy of small solutes, based on a standard thermodynamic integration scheme. The reliability of this new approach has been checked for the properties of solvated methane and of the solvated methane dimer, as well as by performing 10 × 20 ns molecular dynamics (MD) trajectories for three solvated proteins. A long-time stability of the protein structures along the trajectories is observed. Moreover, our method still provides a measure of the protein solvation thermodynamic at the same accuracy as standard Poisson-Boltzman continuum methods. These results show the relevance of our approach and its applicability to massively coupled MD schemes to accurately and intensively explore solvated macromolecule potential energy surfaces.

  8. Phase separation in H2O:N2 mixture - molecular dynamics simulations using atomistic force fields

    Energy Technology Data Exchange (ETDEWEB)

    Maiti, A; Gee, R; Bastea, S; Fried, L

    2006-09-25

    A class II atomistic force field with Lennard-Jones 6-9 nonbond interactions is used to investigate equations of state (EOS) for important high explosive detonation products N{sub 2} and H{sub 2}O in the temperature range 700-2500 K and pressure range 0.1-10 GPa. A standard 6th order parameter-mixing scheme is then employed to study a 2:1 (molar) H{sub 2}O:N{sub 2} mixture, to investigate in particular the possibility of phase-separation under detonation conditions. The simulations demonstrate several important results, including: (1) the accuracy of computed EOS for both N{sub 2} and H{sub 2}O over the entire range of temperature and pressure considered; (2) accurate mixing-demixing phase boundary as compared to experimental data; and (3) the departure of mixing free energy from that predicted by ideal mixing law. The results provide comparison and guidance to state-of-the-art chemical kinetic models.

  9. Reactive force field simulation of proton diffusion in BaZrO{sub 3} using an empirical valence bond approach

    Energy Technology Data Exchange (ETDEWEB)

    Raiteri, Paolo; Gale, Julian D [Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box 1987, Perth, WA 6845 (Australia); Bussi, Giovanni, E-mail: paolo@ivec.org, E-mail: julian@ivec.org [Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste (Italy)

    2011-08-24

    A new reactive force field to describe proton diffusion within the solid oxide fuel cell material BaZrO{sub 3} has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO{sub 3} have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.

  10. Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

    Science.gov (United States)

    Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

    2004-07-15

    Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

  11. A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field.

    Science.gov (United States)

    Xiang, Jin Yu; Ponder, Jay W

    2013-04-05

    A general molecular mechanics (MM) model for treating aqueous Cu(2+) and Zn(2+) ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas-phase tetra- and hexa-aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA-VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA-VB model generates the correct square-planar geometry for gas-phase tetra-aqua Cu(2+) complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA-VB generate results for Zn(2+)-water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six-coordination first solvation shell for both Cu(2+) and Zn(2+) ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. Copyright © 2012 Wiley Periodicals, Inc.

  12. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins.

    Science.gov (United States)

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie; Aspuru-Guzik, Alán; Kleinekathöfer, Ulrich

    2015-08-06

    Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna-Matthews-Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbital (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution.

  13. Muscle co-contraction patterns in robot-mediated force field learning to guide specific muscle group training.

    Science.gov (United States)

    Pizzamiglio, Sara; Desowska, Adela; Shojaii, Pegah; Taga, Myriam; Turner, Duncan L

    2017-01-01

    Muscle co-contraction is a strategy of increasing movement accuracy and stability employed in dealing with force perturbation of movement. It is often seen in neuropathological populations. The direction of movement influences the pattern of co-contraction, but not all movements are easily achievable for populations with motor deficits. Manipulating the direction of the force instead, may be a promising rehabilitation protocol to train movement with use of a co-contraction reduction strategy. Force field learning paradigms provide a well described procedure to evoke and test muscle co-contraction. The aim of this study was to test the muscle co-contraction pattern in a wide range of arm muscles in different force-field directions utilising a robot-mediated force field learning paradigm of motor adaptation. Forty-two participants volunteered to participate in a study utilising robot-mediated force field motor adaptation paradigm with a clockwise or counter-clockwise force field. Kinematics and surface electromyography (EMG) of eight arm muscles were measured. Both muscle activation and co-contraction was earlier and stronger in flexors in the clockwise condition and in extensors in the counter-clockwise condition. Manipulating the force field direction leads to changes in the pattern of muscle co-contraction.

  14. Force field development for actinyl ions via quantum mechanical calculations: an approach to account for many body solvation effects.

    Science.gov (United States)

    Rai, Neeraj; Tiwari, Surya P; Maginn, Edward J

    2012-09-06

    Advances in computational algorithms and methodologies make it possible to use highly accurate quantum mechanical calculations to develop force fields (pair-wise additive intermolecular potentials) for condensed phase simulations. Despite these advances, this approach faces numerous hurdles for the case of actinyl ions, AcO2(n+) (high-oxidation-state actinide dioxo cations), mainly due to the complex electronic structure resulting from an interplay of s, p, d, and f valence orbitals. Traditional methods use a pair of molecules (“dimer”) to generate a potential energy surface (PES) for force field parametrization based on the assumption that many body polarization effects are negligible. We show that this is a poor approximation for aqueous phase uranyl ions and present an alternative approach for the development of actinyl ion force fields that includes important many body solvation effects. Force fields are developed for the UO2(2+) ion with the SPC/Fw, TIP3P, TIP4P, and TIP5P water models and are validated by carrying out detailed molecular simulations on the uranyl aqua ion, one of the most characterized actinide systems. It is shown that the force fields faithfully reproduce available experimental structural data and hydration free energies. Failure to account for solvation effects when generating PES leads to overbinding between UO2(2+) and water, resulting in incorrect hydration free energies and coordination numbers. A detailed analysis of arrangement of water molecules in the first and second solvation shell of UO2(2+) is presented. The use of a simple functional form involving the sum of Lennard-Jones + Coulomb potentials makes the new force field compatible with a large number of available molecular simulation engines and common force fields.

  15. The fast multipole method and point dipole moment polarizable force fields

    Science.gov (United States)

    Coles, Jonathan P.; Masella, Michel

    2015-01-01

    We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.

  16. Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field.

    Science.gov (United States)

    Thaunay, Florian; Dognon, Jean-Pierre; Ohanessian, Gilles; Clavaguéra, Carine

    2015-10-21

    The calculation of infrared spectra by molecular dynamics simulations based on the AMOEBA polarizable force field has recently been demonstrated [Semrouni et al., J. Chem. Theory Comput., 2014, 10, 3190]. While this approach allows access to temperature and anharmonicity effects, band assignment requires additional tools, which we describe in this paper. The Driven Molecular Dynamics approach, originally developed by Bowman, Kaledin et al. [Bowman et al. J. Chem. Phys., 2003, 119, 646, Kaledin et al. J. Chem. Phys., 2004, 121, 5646] has been adapted and associated with AMOEBA. Its advantages and limitations are described. The IR spectrum of the Ac-Phe-Ala-NH2 model peptide is analyzed in detail. In addition to differentiation of conformations by reproducing frequency shifts due to non-covalent interactions, DMD allows visualizing the temperature-dependent vibrational modes.

  17. Force-Field Derivation and Atomistic Simulation of HMX/Graphite Interface and Polycrystal Systems

    Institute of Scientific and Technical Information of China (English)

    龙瑶; 刘永刚; 聂福德; 陈军

    2012-01-01

    Interface is the key issue to understand the performance of composite materials. In this work, we study the interface between octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and graphite, try to find out its contribution to mixture explosives. The work starts from the force-field derivation. We get ab initio based pair potentials across the interface, and then use them to study the interface structural and mechanical properties. A series of large scale molecular dynamics simulations are performed. The structure evolution, energy variation and elastic/plastic transformation of interface and polycrystal systems are calculated. The desensitizing mechanism of graphite to HMX is discussed.

  18. The Fast Multipole Method and Point Dipole Moment Polarizable Force Fields

    CERN Document Server

    Coles, Jonathan P

    2014-01-01

    We present a momentum conserving implementation of the fast multipole method for computing coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected $O(N)$ scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using both a standard integrator and a multiple time step one. Our tests show the applicability of FMM combined with state-of-the-art chemical models in molecular dynamical systems.

  19. Modeling of Centrifugal Force Field and the Effect on Filling and Solidification in Centrifugal Casting

    Science.gov (United States)

    Sheng, Wenbin; Ma, Chunxue; Gu, Wanli

    2011-06-01

    Based on the steady flow in a tube, a mathematical model has been established for the consideration of centrifuging force field by combining the equations of continuity, conservation of momentum and general energy. Effects of centrifugal field on the filling and solidification are modeled by two accessional terms: centrifugal force and Chorios force. In addition, the transfer of heat by convection is considered to achieve a coupling calculation of velocity field and temperature field. The solution of pressure item is avoided by introducing the stream function ψ(x,y) and the eddy function ξ(x,y). Corresponding difference formats for the simultaneous equations of centrifugal filling, the accessional terms and the solidifying latent heat have been established by the finite difference technique. Furthermore, the centrifugal filling and solidification processes in a horizontal tube are summarized to interpret the mechanism by which internal defects are formed in centrifugal castings.

  20. Combining simulations and solution experiments as a paradigm for RNA force field refinement

    CERN Document Server

    Cesari, Andrea; Bussi, Giovanni

    2016-01-01

    Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with experimental data. We here propose a scheme based on the maximum entropy principle to combine simulations with bulk experiments. In the proposed scheme the noise arising from both the measurements and the forward models used to back calculate the experimental observables is explicitly taken into account. The method is tested on RNA nucleosides and is then used to construct chemically consistent corrections to the Amber RNA force field that allow a large set of experimental data on nucleosides and dinucleosides to be correctly reproduced. The transferability of these corrections is assessed against independent data on tetranucleotides and displays a previously unreported agreement with experiments. This procedure can be applied to enforce multiple experimental d...

  1. Mold Filling Behavior of Melts with Different Viscosity under Centrifugal Force Field

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Recently proposed mathematical model for mold filling processes under centrifugal force field conditions and the computer codes were first tested through the sample simulation of gravity mold filling process for a benchmark plate-casting, which were compared with quoted experimental observations. The model and the developed computer program were then applied to the numerical simulation of centrifugal field mold filling processes for a thin-section casting with a titanium alloy melt of assumed viscosity of 1.2 and 12.0 mm2/s, respectively. The computation result comparison shows that the flow behaviors of the filling melts are basically similar to each other although the less viscous melt tends to fill into the thin section casting cavity faster.

  2. A coarse-grain force field for RDX: Density dependent and energy conserving

    Science.gov (United States)

    Moore, Joshua D.; Barnes, Brian C.; Izvekov, Sergei; Lísal, Martin; Sellers, Michael S.; Taylor, DeCarlos E.; Brennan, John K.

    2016-03-01

    We describe the development of a density-dependent transferable coarse-grain model of crystalline hexahydro-1,3,5-trinitro-s-triazine (RDX) that can be used with the energy conserving dissipative particle dynamics method. The model is an extension of a recently reported one-site model of RDX that was developed by using a force-matching method. The density-dependent forces in that original model are provided through an interpolation scheme that poorly conserves energy. The development of the new model presented in this work first involved a multi-objective procedure to improve the structural and thermodynamic properties of the previous model, followed by the inclusion of the density dependency via a conservative form of the force field that conserves energy. The new model accurately predicts the density, structure, pressure-volume isotherm, bulk modulus, and elastic constants of the RDX crystal at ambient pressure and exhibits transferability to a liquid phase at melt conditions.

  3. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.

    Science.gov (United States)

    Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

    2015-04-14

    A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed.

  4. Second Law Violations by Means of a Stratification of Temperature Due to Force Fields

    Science.gov (United States)

    Trupp, Andreas

    2002-11-01

    In 1868 J.C. Maxwell proved that a perpetual motion machine of the second kind would become possible, if the equilibrium temperature in a vertical column of gas subject to gravity were a function of height. However, Maxwell had claimed that the temperature had to be the same at all points of the column. So did Boltzmann. Their opponent was Loschmidt. He claimed that the equilibrium temperature declined with height, and that a perpetual motion machine of the second kind operating by means of such column was compatible with the second law of thermodynamics. Extending the general idea behind Loschmidt's concept to other force fields, gravity can be replaced by molecular forces acting on molecules that try to escape from the surface of a liquid into the vapor space. Experiments proving the difference of temperature between the liquid and the vapor phase were conducted in the 19th century already.

  5. Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes

    DEFF Research Database (Denmark)

    Jakobsen, Sofie; Bereau, Tristan; Meuwly, Markus

    2015-01-01

    The performance of multipole (MTP) and point charge (PC) force fields in classical molecular dynamics (MD) simulations of condensed-phase systems for both equilibrium and dynamical quantities is compared. MTP electrostatics provides an improved description of the anisotropic electrostatic potential......, which is especially important to describe key, challenging interactions, such as lone pairs, π-interactions, and hydrogen bonds. These chemical environments are probed by focusing on the hydration properties of two molecules: N-methylacetamide and phenyl bromide. Both, equilibrium and dynamical......, quantities are affected by the quality of the electrostatic model. The alteration of the first solvation shell in MTP simulations is validated by comparing with lifetimes and correlation times of solute–solvent interactions from experiment. The improved dynamical behavior found in the MTP simulations...

  6. Predictions for water clusters from a first-principles two- and three-body force field.

    Science.gov (United States)

    Góra, Urszula; Cencek, Wojciech; Podeszwa, Rafał; van der Avoird, Ad; Szalewicz, Krzysztof

    2014-05-21

    A new rigid-monomer three-body potential has been developed for water by fitting it to more than 70 thousand trimer interaction energies computed ab initio using coupled-cluster methods and augmented triple-zeta-quality basis sets. This potential was used together with a modified form of a previously developed two-body potential and with a polarization model of four- and higher-body interactions to predict the energetics of the water trimer, hexamer, and 24-mer. Despite using the rigid-monomer approximation, these predictions agree better with flexible-monomer benchmarks than published results obtained with flexible-monomer force fields. An unexpected finding of our work is that simple polarization models predict four-body interactions to within a few percent, whereas for three-body interactions these models are known to have errors on the order of 50%.

  7. Spatial information recognizing of ocean eddies based on virtual force field and its application

    Institute of Scientific and Technical Information of China (English)

    LI Ce; DU Yunyan; SU Fenzhen; YANG Xiaomei; XU Jun

    2007-01-01

    A new approach to detecting ocean eddies automatically from remote sensing imageries based on the ocean eddy's eigen-pattern in remote sensing imagery and "force field-based shape extracting method" is proposed. First, the analysis on extracting eddies' edges from remote sensing imagery using conventional edge detection arithmetic operators is performed and returns digitized vector edge data as a result. Second, attraction forces and fusion forces between edge curves were analyzed and calculated based on the vector eddy edges. Thirdly, the virtual significant spatial patterns of eddy were detected automatically using iterative repetition followed by optimized rule. Finally, the spatial form auto-detection of different types of ocean eddies was done using satellite images.The study verified that this is an effective way to identify and detect the ocean eddy with a complex form.

  8. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  9. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.

    Science.gov (United States)

    Arnautova, Yelena A; Vorobjev, Yury N; Vila, Jorge A; Scheraga, Harold A

    2009-10-01

    Availability of energy functions which can discriminate native-like from non-native protein conformations is crucial for theoretical protein structure prediction and refinement of low-resolution protein models. This article reports the results of benchmark tests for scoring functions based on two all-atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent-accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent-accessible surface area model of Ooi et al. (Proc Natl Acad Sci USA 1987;84:3086-3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/FAMBEpH). Short Monte Carlo-with-Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native-like and non-native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native-like structures with C(alpha) root-mean-square-deviations below 3.5 A as lowest-energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein-solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native-like structures cannot be discriminated as those with low

  10. Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations

    Science.gov (United States)

    Demerdash, Omar; Mao, Yuezhi; Liu, Tianyi; Head-Gordon, Martin; Head-Gordon, Teresa

    2017-10-01

    In this work, we evaluate the accuracy of the classical AMOEBA model for representing many-body interactions, such as polarization, charge transfer, and Pauli repulsion and dispersion, through comparison against an energy decomposition method based on absolutely localized molecular orbitals (ALMO-EDA) for the water trimer and a variety of ion-water systems. When the 2- and 3-body contributions according to the many-body expansion are analyzed for the ion-water trimer systems examined here, the 3-body contributions to Pauli repulsion and dispersion are found to be negligible under ALMO-EDA, thereby supporting the validity of the pairwise-additive approximation in AMOEBA's 14-7 van der Waals term. However AMOEBA shows imperfect cancellation of errors for the missing effects of charge transfer and incorrectness in the distance dependence for polarization when compared with the corresponding ALMO-EDA terms. We trace the larger 2-body followed by 3-body polarization errors to the Thole damping scheme used in AMOEBA, and although the width parameter in Thole damping can be changed to improve agreement with the ALMO-EDA polarization for points about equilibrium, the correct profile of polarization as a function of intermolecular distance cannot be reproduced. The results suggest that there is a need for re-examining the damping and polarization model used in the AMOEBA force field and provide further insights into the formulations of polarizable force fields in general.

  11. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations

    Science.gov (United States)

    Cai, Kaicong; Zheng, Xuan; Du, Fenfen

    2017-08-01

    The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.

  12. Accurate AB Initio Calculation of Anharmonic Force Fields and Spectroscopic Constants of Small Polyatomic Molecules

    Science.gov (United States)

    Martin, Jan M. L.

    The quartic force fields of a number of small polyatomic molecules (specifically, rm H _2O, NH_2, NH_3, CH_4, BH_3, BeH_2, H_2CO, N_2O, CO_2, CS_2, OCS, H_2S, FNO, ClNO, and H_2CS) have been computed ab initio using large basis sets and augmented coupled cluster methods. It has been established throughout that harmonic and fundamental frequencies can consistently be reproduced to within about 10 cm^{ -1} of experimental using spdf basis sets, except in such inherently problematic cases as the umbrella motion in NH_3; such problems are solved by recomputing the harmonic frequencies with an spdf g basis set. Coupled cluster frequencies using small basis sets of spd quality agree surprisingly well with experiment (mean absolute error of 26 cm^ {-1}), but bond distances are generally seriously overestimated. Using spdf basis sets, they are consistently overestimated by 0.002 and 0.006-7 A for single and multiple bonds, respectively; for spdf g basis sets this drops to 0.001 and 0.003-4 A, respectively. Geometries and harmonic frequencies for highly polar fluorine compounds such as HF and FNO are qualitatively wrong unless special anion functions are added to the fluorine basis set. Anharmonicity, rovibrational coupling, and centrifugal distortion constants are consistently predicted well; the anharmonic portions of the computed force fields are probably more reliable than their experimental counterparts in many cases. Remaining errors in the computed geometries and harmonic frequencies are shown to be almost entirely due to a combination of core correlation and residual deficiencies in the electron correlation treatment. A 3-term correction for remaining basis set incompleteness to computed total atomization energies is proposed by the author, and is shown to result in mean absolute errors of as little as 0.5 kcal/mol for spdf g basis sets. Example applications on rm HCO^+, HOC^+, B_2C, BCN, and BNC testify to the predictive power of the methods used in this work.

  13. Molecular Dynamics Simulation of Cross-Linked Epoxy Polymers: the Effect of Force Field on the Estimation of Properties

    Directory of Open Access Journals (Sweden)

    B. Arab

    2013-03-01

    Full Text Available In this paper, the molecular dynamics method was used to calculate the physical and mechanical properties of the cross-linked epoxy polymer composed of diglycidyl ether of bisphenol-A (DGEBA as resin and diethylenetriamine (DETA as curing agent. Calculation of the properties was performed using the constant-strain (static approach. A series of independent simulations were carried out based on four widely used force fields; COMPASS, PCFF, UFF and Dreiding. Proper comparisons between the results and also with experimental observations were made to find the most suitable force field for molecular dynamics simulation of polymer materials.

  14. Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations.

    Science.gov (United States)

    Schwörer, Magnus; Breitenfeld, Benedikt; Tröster, Philipp; Bauer, Sebastian; Lorenzen, Konstantin; Tavan, Paul; Mathias, Gerald

    2013-06-28

    Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

  15. Protein simulations in fluids: coupling the OPEP coarse-grained force field with hydrodynamics

    Science.gov (United States)

    Sterpone, Fabio; Derreumaux, Philippe; Melchionna, Simone

    2017-01-01

    A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level, is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modelling systems made up to thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multi-scale approach are also discussed. PMID:26574390

  16. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    Science.gov (United States)

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-05

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

  17. The ELBA force field for coarse-grain modeling of lipid membranes.

    Directory of Open Access Journals (Sweden)

    Mario Orsi

    Full Text Available A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (ε(r = 1. Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC and dioleoylphosphatidylethanolamine (DOPE in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids; this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities.

  18. A fully ab initio quartic force field of spectroscopic quality for $SO_3$

    CERN Document Server

    Martin, J M L

    1999-01-01

    The quartic force field of SO$_3$ was computed fully ab initio using coupled cluster (CCSD(T)) methods and basis sets of up to $spdfgh$ quality. The effect of inner-shell correlation was taken into account. The addition of tight $d$ functions is found to be essential for accurate geometries and harmonic frequencies. The equilibrium geometry and vibrational fundamentals are reproduced to within 0.0003 Å and (on average) 1.15 cm^{-1}, respectively. We recommend the following revised values for the harmonic frequencies: $\\omega_1 = 1082.7, \\omega_2 = 502.6, \\omega_3 = 1415.4, \\omega_4 = 534.0 cm^{-1}$. In addition, we have shown that the addition of inner polarization functions to second-row elements is highly desirable even with more approximate methods like B3LYP, and greatly improves the quality of computed geometries and harmonic frequencies of second-row compounds at negligible extra computational cost. For larger such molecules, the B3LYP/VTZ+1 level of theory should be a very good compromise between accu...

  19. Determining polarizable force fields with electrostatic potentials from quantum mechanical linear response theory.

    Science.gov (United States)

    Wang, Hao; Yang, Weitao

    2016-06-14

    We developed a new method to calculate the atomic polarizabilities by fitting to the electrostatic potentials (ESPs) obtained from quantum mechanical (QM) calculations within the linear response theory. This parallels the conventional approach of fitting atomic charges based on electrostatic potentials from the electron density. Our ESP fitting is combined with the induced dipole model under the perturbation of uniform external electric fields of all orientations. QM calculations for the linear response to the external electric fields are used as input, fully consistent with the induced dipole model, which itself is a linear response model. The orientation of the uniform external electric fields is integrated in all directions. The integration of orientation and QM linear response calculations together makes the fitting results independent of the orientations and magnitudes of the uniform external electric fields applied. Another advantage of our method is that QM calculation is only needed once, in contrast to the conventional approach, where many QM calculations are needed for many different applied electric fields. The molecular polarizabilities obtained from our method show comparable accuracy with those from fitting directly to the experimental or theoretical molecular polarizabilities. Since ESP is directly fitted, atomic polarizabilities obtained from our method are expected to reproduce the electrostatic interactions better. Our method was used to calculate both transferable atomic polarizabilities for polarizable molecular mechanics' force fields and nontransferable molecule-specific atomic polarizabilities.

  20. Semi-quartic force fields retrieved from multi-mode expansions: Accuracy, scaling behavior, and approximations

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Raghunathan [Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel (Switzerland); Rauhut, Guntram, E-mail: rauhut@theochem.uni-stuttgart.de [Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany)

    2015-04-21

    Semi-quartic force fields (QFF) rely on a Taylor-expansion of the multi-dimensional Born-Oppenheimer potential energy surface (PES) and are frequently used within the calculation of anharmonic vibrational frequencies based on 2nd order vibrational perturbation theory (VPT2). As such they are usually determined by differentiation of the electronic energy with respect to the nuclear coordinates. Alternatively, potential energy surfaces can be expanded in terms of multi-mode expansions, which typically do not require any derivative techniques. The computational effort to retrieve QFF from size-reduced multi-mode expansions has been studied and has been compared with standard Taylor-expansions. As multi-mode expansions allow for the convenient introduction of subtle approximations, these will be discussed in some detail. In addition, a preliminary study about the applicability of a generalized Duschinsky transformation to QFFs is provided. This transformation allows for the efficient evaluation of VPT2 frequencies of isotopologues from the PES of the parent compound and thus avoids the recalculation of PESs in different axes systems.

  1. Penetration Barrier of Water through Graphynes' Pores: First-Principles Predictions and Force Field Optimization.

    Science.gov (United States)

    Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I; Campos-Martínez, José; Pirani, Fernando; Giorgi, Giacomo; Yamashita, Koichi

    2014-02-20

    Graphynes are novel two-dimensional carbon-based materials that have been proposed as molecular filters, especially for water purification technologies. We carry out first-principles electronic structure calculations at the MP2C level of theory to assess the interaction between water and graphyne, graphdiyne, and graphtriyne pores. The computed penetration barriers suggest that water transport is unfeasible through graphyne while being unimpeded for graphtriyne. For graphdiyne, with a pore size almost matching that of water, a low barrier is found that in turn disappears if an active hydrogen bond with an additional water molecule on the opposite side of the opening is considered. Thus, in contrast with previous determinations, our results do not exclude graphdiyne as a promising membrane for water filtration. In fact, present calculations lead to water permeation probabilities that are 2 orders of magnitude larger than estimations based on common force fields. A new pair potential for the water-carbon noncovalent component of the interaction is proposed for molecular dynamics simulations involving graphdiyne and water.

  2. SAFT-γ force field for the simulation of molecular fluids: 2. Coarse-grained models of greenhouse gases, refrigerants, and long alkanes.

    Science.gov (United States)

    Avendaño, Carlos; Lafitte, Thomas; Adjiman, Claire S; Galindo, Amparo; Müller, Erich A; Jackson, George

    2013-03-07

    In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, and E. A. Müller, J. Phys. Chem. B2011, 115, 11154] we introduced the SAFT-γ force field for molecular simulation of fluids. In our approach, a molecular-based equation of state (EoS) is used to obtain coarse-grained (CG) intermolecular potentials that can then be employed in molecular simulation over a wide range of thermodynamic conditions of the fluid. The macroscopic experimental data for the vapor-liquid equilibria (saturated liquid density and vapor pressure) of a given system are represented with the SAFT-VR Mie EoS and used to estimate effective intermolecular parameters that provide a good description of the thermodynamic properties by exploring a wide parameter space for models based on the Mie (generalized Lennard-Jones) potential. This methodology was first used to develop a simple single-segment CG Mie model of carbon dioxide (CO2) which allows for a reliable representation of the fluid-phase equilibria (for which the model was parametrized), as well as an accurate prediction of other properties such as the enthalpy of vaporization, interfacial tension, supercritical density, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thomson coefficient, and speed of sound). In our current paper, the methodology is further applied and extended to develop effective SAFT-γ CG Mie force fields for some important greenhouse gases including carbon tetrafluoride (CF4) and sulfur hexafluoride (SF6), modeled as simple spherical molecules, and for long linear alkanes including n-decane (n-C10H22) and n-eicosane (n-C20H42), modeled as homonuclear chains of spherical Mie segments. We also apply the SAFT-γ methodology to obtain a CG homonuclear two-segment Mie intermolecular potential for the more challenging polar and asymmetric compound 2,3,3,3-tetrafluoro-1-propene (HFO-1234yf), a novel replacement

  3. Genetic algorithms coupled with quantum mechanics for refinement of force fields for RNA simulation: a case study of glycosidic torsions in the canonical ribonucleosides.

    Science.gov (United States)

    Kato, Rodrigo B; Silva, Frederico T; Pappa, Gisele L; Belchior, Jadson C

    2015-01-28

    We report the use of genetic algorithms (GA) as a method to refine force field parameters in order to determine RNA energy. Quantum-mechanical (QM) calculations are carried out for the isolated canonical ribonucleosides (adenosine, guanosine, cytidine and uridine) that are taken as reference data. In this particular study, the dihedral and electrostatic energies are reparametrized in order to test the proposed approach, i.e., GA coupled with QM calculations. Overall, RMSE comparison with recent published results for ribonucleosides energies shows an improvement, on average, of 50%. Finally, the new reparametrized potential energy function is used to determine the spatial structure of RNA (PDB code ) that was not taken into account in the parametrization process. This structure was improved about 82% comparable with previously published results.

  4. Application of the Modified Urey-Bradley-Shimanouchi Force field of α-D-Glucopyranose and β-D-Fructopyranose to Predict the Vibrational Spectra of Disaccharides

    Science.gov (United States)

    Gafour, H. M.; Sekkal-Rahal, M.; Sail, K.

    2014-01-01

    The vibrational frequencies of the disaccharide isomaltulose in the solid state have been reproduced in the 50-4000 cm-1 range. The modified Urey-Bradley-Shimanouchi force field was used, combined with an inter molecular potential energy function that includes van der Waals interactions, electrostatic terms, and an explicit hydrogen bond function. The force constants previously established for α-D-glucopyranose and β-D-fructo pyranose, as well as the crystallographic data of isomaltulose monohydrate, were the starting parameters for the present work. The vibrational frequencies of isomaltulose were calculated and assigned to the experimentally observed vibrational frequencies. Overall, there was good agreement between the observed and calculated frequencies with an average error of 4 cm-1. Furthermore, good agreement was found between our calculated results and the vibration spectra of other disaccharides and monosaccharides.

  5. Improved Parameterization of Amine-Carboxyate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

    CERN Document Server

    Yoo, Jejoong

    2015-01-01

    Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which have been developed and validated using relatively short simulations of small molecules---become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge--charge interactions. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine--carboxylate and amine--phosphate interactions, which brings MD simulations of basic peptide-mediated nucleic acids assemblies and lipid bilayer membranes in better agreement with experiment. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing additional artifacts.

  6. Molecular dynamic study of Shock wave response of bulk amorphous polyvinyl chloride: effect of chain length and force field

    Science.gov (United States)

    Neogi, Anupam; Mitra, Nilanjan

    2015-06-01

    Atomistic molecular dynamics in conjunction with multi-scale shock technique is utilized to investigate shock wave response of bulk amorphous polyvinyl chloride. Dependence of chain length on physical and mechanical behaviour of polymeric material at ambient condition of temperature and pressure are well known but unknown for extreme conditions. Non-reactive force fields PCFF, COMPASS and PCFF+ were used to determine applicability of the force field for the study of the material subjected to shock loads. Several samples of PVC with various chain lengths were subjected to a range of shock compression from 1.5-10.0 km/s. Even though dependence of chain length was observed for lower shock strengths but was not for intense shock loads. The principle Hugoniot points, calculated by applying hydrostatic Rankine-Hugoniot equations and as well as multi-scale shock technique, were compared against LASL experimental shock data, demonstrating superior performance of PCFF+ force-field over PCFF and COMPASS. Shock induced melting characteristic and vibrational spectroscopic study were conducted and compared with experimental data to observe differences in response with relation to different force fields, chain length of the material for different shock intensities.

  7. AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

    Science.gov (United States)

    2015-01-01

    Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer’s disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code. PMID:24931227

  8. AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins.

    Science.gov (United States)

    Santos-Martins, Diogo; Forli, Stefano; Ramos, Maria João; Olson, Arthur J

    2014-08-25

    Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in diseases such as cancer, heart disease, bacterial infection, and Alzheimer's disease. In most cases a drug molecule targeting such enzymes establishes an interaction that coordinates with the zinc ion. Thus, accurate prediction of the interaction of ligands with zinc is an important aspect of computational docking and virtual screening against zinc containing proteins. We have extended the AutoDock force field to include a specialized potential describing the interactions of zinc-coordinating ligands. This potential describes both the energetic and geometric components of the interaction. The new force field, named AutoDock4Zn, was calibrated on a data set of 292 crystal complexes containing zinc. Redocking experiments show that the force field provides significant improvement in performance in both free energy of binding estimation as well as in root-mean-square deviation from the crystal structure pose. The new force field has been implemented in AutoDock without modification to the source code.

  9. Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride).

    Science.gov (United States)

    Lachet, V; Teuler, J-M; Rousseau, B

    2015-01-08

    A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.

  10. CO2在LTA型和FAU型沸石分子筛中吸附的力场研究%Study on adsorption force field of CO2 in LTA and FAU zeolites

    Institute of Scientific and Technical Information of China (English)

    陈树军; 付越; 黄毅雄

    2016-01-01

    采用巨正则系综的蒙特卡罗法,利用几种通用力场对LTA型4A分子筛吸附CO2进行模拟研究,基于Dreiding力场分析力场参数σ和ε对模拟结果的影响,得到适用于4A分子筛吸附CO2的准确Dreiding力场参数。将该力场参数应用到LTA型5A分子筛吸附模拟中,得到5A分子筛吸附模拟的力场参数。最后将4A分子筛吸附CO2的力场参数应用到FAU型13X分子筛的吸附模拟中。结果表明:模拟结果与实验数据吻合较好,分子筛阳离子的改变对吸附力场影响较大,而分子筛结构对力场的影响相对较小。与13X具有同种阳离子的4A分子筛力场参数可直接作为13X分子筛的力场,具有通用性。%Adsorptions of CO2 in 4A zeolites of LTA was investigated by grand canonical Monte Carlo (GCMC) method. The influences of σ and εparameters in Dreiding force field on the simulation results were analyzed by GCMC method. The opti-mized force fields were obtained by fitting the experimental data of 4A zeolites of LTA. Then the CO2 adsorption isotherm on 5A zeolites of LTA was computed based on the obtained force fields. According to the influences of σ and ε parameters in Dreiding force field on the simulation results, the suitable force field parameters of CO2 adsorption on 5A zeolites were quick-ly obtained. Finally, CO2 adsorption isotherm on 13X zeolites of FAU was computed by the optimized force field parameters. The results show that the simulated results are in a good agreement with the experimental data. The change of cation in mo-lecular sieve has a greater influence on the adsorption force field than the molecular sieve structure, the optimized force field parameters which describe the 4A zeolites of LTA well, are suitable for the CO2 adsorption on 13X zeolites of FAU. The con-clusions are versatility.

  11. Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold.

    Science.gov (United States)

    Hughes, Zak E; Wright, Louise B; Walsh, Tiffany R

    2013-10-29

    The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively

  12. A bidirectional brain-machine interface algorithm that approximates arbitrary force-fields.

    Directory of Open Access Journals (Sweden)

    Alessandro Vato

    Full Text Available We examine bidirectional brain-machine interfaces that control external devices in a closed loop by decoding motor cortical activity to command the device and by encoding the state of the device by delivering electrical stimuli to sensory areas. Although it is possible to design this artificial sensory-motor interaction while maintaining two independent channels of communication, here we propose a rule that closes the loop between flows of sensory and motor information in a way that approximates a desired dynamical policy expressed as a field of forces acting upon the controlled external device. We previously developed a first implementation of this approach based on linear decoding of neural activity recorded from the motor cortex into a set of forces (a force field applied to a point mass, and on encoding of position of the point mass into patterns of electrical stimuli delivered to somatosensory areas. However, this previous algorithm had the limitation that it only worked in situations when the position-to-force map to be implemented is invertible. Here we overcome this limitation by developing a new non-linear form of the bidirectional interface that can approximate a virtually unlimited family of continuous fields. The new algorithm bases both the encoding of position information and the decoding of motor cortical activity on an explicit map between spike trains and the state space of the device computed with Multi-Dimensional-Scaling. We present a detailed computational analysis of the performance of the interface and a validation of its robustness by using synthetic neural responses in a simulated sensory-motor loop.

  13. Fast divide-and-conquer algorithm for evaluating polarization in classical force fields

    Science.gov (United States)

    Nocito, Dominique; Beran, Gregory J. O.

    2017-03-01

    Evaluation of the self-consistent polarization energy forms a major computational bottleneck in polarizable force fields. In large systems, the linear polarization equations are typically solved iteratively with techniques based on Jacobi iterations (JI) or preconditioned conjugate gradients (PCG). Two new variants of JI are proposed here that exploit domain decomposition to accelerate the convergence of the induced dipoles. The first, divide-and-conquer JI (DC-JI), is a block Jacobi algorithm which solves the polarization equations within non-overlapping sub-clusters of atoms directly via Cholesky decomposition, and iterates to capture interactions between sub-clusters. The second, fuzzy DC-JI, achieves further acceleration by employing overlapping blocks. Fuzzy DC-JI is analogous to an additive Schwarz method, but with distance-based weighting when averaging the fuzzy dipoles from different blocks. Key to the success of these algorithms is the use of K-means clustering to identify natural atomic sub-clusters automatically for both algorithms and to determine the appropriate weights in fuzzy DC-JI. The algorithm employs knowledge of the 3-D spatial interactions to group important elements in the 2-D polarization matrix. When coupled with direct inversion in the iterative subspace (DIIS) extrapolation, fuzzy DC-JI/DIIS in particular converges in a comparable number of iterations as PCG, but with lower computational cost per iteration. In the end, the new algorithms demonstrated here accelerate the evaluation of the polarization energy by 2-3 fold compared to existing implementations of PCG or JI/DIIS.

  14. Realistic sampling of amino acid geometries for a multipolar polarizable force field.

    Science.gov (United States)

    Hughes, Timothy J; Cardamone, Salvatore; Popelier, Paul L A

    2015-09-15

    The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X-ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF.

  15. Thermodynamic properties of hydrogen dissociation reaction from the small system method and reactive force field ReaxFF

    Science.gov (United States)

    Trinh, Thuat T.; Meling, Nora; Bedeaux, Dick; Kjelstrup, Signe

    2017-03-01

    We present thermodynamic properties of the H2 dissociation reaction by means of the Small System Method (SSM) using Reactive Force Field (ReaxFF) simulations. Thermodynamic correction factors, partial molar enthalpies and heat capacities of the reactant and product were obtained in the high temperature range; up to 30,000 K. The results obtained from the ReaxFF potential agree well with previous results obtained with a three body potential (TBP). This indicates that the popular reactive force field method can be combined well with the newly developed SSM in realistic simulations of chemical reactions. The approach may be useful in the study of heat and mass transport in combination with chemical reactions.

  16. Simulating the Activation of Voltage Sensing Domain for a Voltage-Gated Sodium Channel Using Polarizable Force Field.

    Science.gov (United States)

    Sun, Rui-Ning; Gong, Haipeng

    2017-03-02

    Voltage-gated sodium (NaV) channels play vital roles in the signal transduction of excitable cells. Upon activation of a NaV channel, the change of transmembrane voltage triggers conformational change of the voltage sensing domain, which then elicits opening of the pore domain and thus allows an influx of Na(+) ions. Description of this process with atomistic details is in urgent demand. In this work, we simulated the partial activation process of the voltage sensing domain of a prokaryotic NaV channel using a polarizable force field. We not only observed the conformational change of the voltage sensing domain from resting to preactive state, but also rigorously estimated the free energy profile along the identified reaction pathway. Comparison with the control simulation using an additive force field indicates that voltage-gating thermodynamics of NaV channels may be inaccurately described without considering the electrostatic polarization effect.

  17. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    Science.gov (United States)

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  18. Technologies for Developing Predictive Atomistic and Coarse-Grained Force Fields for Ionic Liquid Property Prediction

    Science.gov (United States)

    2008-07-29

    Butanesulfonate (some parameters for 1-ethyl-3-methylimidazolium cation taken from the work of Cadena et al).2 I. Intramolecular terms (bond, angles...parameters for the anions of (A) and (B). Dihedral parameters for the cation of (B) were taken directly from the work of Cadena et al.2 Dihedral...19586. 2 Cadena , C.; Anthony, J. L.; Shah, J. K.; Morrow, T. I.; Brennecke, J. F.; Maginn, E. J. J. Am. Chem. Soc., 2004, 126, 5300 3 Schmidt

  19. Towards time-dependent, non-equilibrium charge-transfer force fields: Contact electrification and history-dependent dissociation limits

    OpenAIRE

    Dapp, Wolf B.; Müser, Martin H.

    2013-01-01

    Force fields uniquely assign interatomic forces for a given set of atomic coordinates. The underlying assumption is that electrons are in their quantum-mechanical ground state or in thermal equilibrium. However, there is an abundance of cases where this is unjustified because the system is only locally in equilibrium. In particular, the fractional charges of atoms, clusters, or solids tend to not only depend on atomic positions but also on how the system reached its state. For example, the ch...

  20. Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

    OpenAIRE

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-01-01

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic sta...

  1. Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

    Science.gov (United States)

    Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

    2014-02-01

    The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine.

  2. R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

    Science.gov (United States)

    Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Élodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

    2008-01-01

    The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. PMID:17962302

  3. Quantum mechanics based force field for carbon (QMFF-Cx) validated to reproduce the mechanical and thermodynamics properties of graphite

    Science.gov (United States)

    Pascal, Tod A.; Karasawa, Naoki; Goddard, William A.

    2010-10-01

    As assemblies of graphene sheets, carbon nanotubes, and fullerenes become components of new nanotechnologies, it is important to be able to predict the structures and properties of these systems. A problem has been that the level of quantum mechanics practical for such systems (density functional theory at the PBE level) cannot describe the London dispersion forces responsible for interaction of the graphene planes (thus graphite falls apart into graphene sheets). To provide a basis for describing these London interactions, we derive the quantum mechanics based force field for carbon (QMFF-Cx) by fitting to results from density functional theory calculations at the M06-2X level, which demonstrates accuracies for a broad class of molecules at short and medium range intermolecular distances. We carried out calculations on the dehydrogenated coronene (C24) dimer, emphasizing two geometries: parallel-displaced X (close to the observed structure in graphite crystal) and PD-Y (the lowest energy transition state for sliding graphene sheets with respect to each other). A third, eclipsed geometry is calculated to be much higher in energy. The QMFF-Cx force field leads to accurate predictions of available experimental mechanical and thermodynamics data of graphite (lattice vibrations, elastic constants, Poisson ratios, lattice modes, phonon dispersion curves, specific heat, and thermal expansion). This validates the use of M06-2X as a practical method for development of new first principles based generations of QMFF force fields.

  4. Physical properties at the base for the development of an all-atom force field for ethylene glycol.

    Science.gov (United States)

    Szefczyk, Borys; Cordeiro, M Natália D S

    2011-03-31

    Ethylene glycol, the simplest of the diols, is a popular solvent, an antifreeze agent, a coolant, and a precursor in polymer production. In molecular modeling it is a model compound used to develop potentials for complex systems, like sugars. Despite the fact that many force fields for ethylene glycol exist in the literature, only few of them have been designed to reproduce the macroscopic properties of glycol and its mixtures, and rather more attention has been paid to the microscopic structure of the liquid. Those potentials that reproduce the properties accurately, apply also nonstandard fudge factors, therefore are not fully compatible with any popular force field. In this paper, we present a new potential for ethylene glycol, based on the OPLS all-atom force field and fully compatible with it, as well as with popular models for water. This potential is carefully validated against a broad range of physical properties measured experimentally and published in the literature. These properties include the density, expansion coefficient, compressibility, enthalpy of vaporization, surface tension, self-diffusion coefficient, and viscosity. Therefore, the potential presented here may be used in simulations of not only pure glycol but also mixtures with water, organic solvents, ionic liquids, phase interfaces, etc.

  5. Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

    Energy Technology Data Exchange (ETDEWEB)

    Trément, Sébastien; Rousseau, Bernard, E-mail: bernard.rousseau@u-psud.fr [Laboratoire de Chimie-Physique, UMR 8000 CNRS, Université Paris-Sud, Orsay (France); Schnell, Benoît; Petitjean, Laurent; Couty, Marc [Manufacture Française des Pneumatiques MICHELIN, Centre de Ladoux, 23 place des Carmes, 63000 Clermont-Ferrand (France)

    2014-04-07

    We apply operational procedures available in the literature to the construction of coarse-grained conservative and friction forces for use in dissipative particle dynamics (DPD) simulations. The full procedure rely on a bottom-up approach: large molecular dynamics trajectories of n-pentane and n-decane modeled with an anisotropic united atom model serve as input for the force field generation. As a consequence, the coarse-grained model is expected to reproduce at least semi-quantitatively structural and dynamical properties of the underlying atomistic model. Two different coarse-graining levels are studied, corresponding to five and ten carbon atoms per DPD bead. The influence of the coarse-graining level on the generated force fields contributions, namely, the conservative and the friction part, is discussed. It is shown that the coarse-grained model of n-pentane correctly reproduces self-diffusion and viscosity coefficients of real n-pentane, while the fully coarse-grained model for n-decane at ambient temperature over-predicts diffusion by a factor of 2. However, when the n-pentane coarse-grained model is used as a building block for larger molecule (e.g., n-decane as a two blobs model), a much better agreement with experimental data is obtained, suggesting that the force field constructed is transferable to large macro-molecular systems.

  6. R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries.

    Science.gov (United States)

    Dupradeau, François-Yves; Cézard, Christine; Lelong, Rodolphe; Stanislawiak, Elodie; Pêcher, Julien; Delepine, Jean Charles; Cieplak, Piotr

    2008-01-01

    The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications.

  7. Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

    Science.gov (United States)

    Kenney, Ian M.; Beckstein, Oliver; Iorga, Bogdan I.

    2016-11-01

    All-atom molecular dynamics simulations were used to predict water-cyclohexane distribution coefficients D_{cw} of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in log D_{cw} of almost 4 log units and an overall signed error of -3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental D_{cw} data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.

  8. R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

    Science.gov (United States)

    Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

    2011-01-01

    R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs. PMID:21609950

  9. R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

    Science.gov (United States)

    Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

    2011-07-01

    R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

  10. Sensitivity of morphology prediction to the force field: Paracetamol as an example

    NARCIS (Netherlands)

    Cuppen, H.M.; Day, G.M.; Verwer, P.; Meekes, H.L.M.

    2004-01-01

    The growth morphology of paracetamol is known to show a strong supersaturation dependence. Most morphology prediction methods, like the attachment energy method, cannot include this dependence in their prediction. Monte Carlo simulations are able to use the supersaturation as an input parameter and

  11. Impact of online visual feedback on motor acquisition and retention when learning to reach in a force field.

    Science.gov (United States)

    Batcho, C S; Gagné, M; Bouyer, L J; Roy, J S; Mercier, C

    2016-11-19

    When subjects learn a novel motor task, several sources of feedback (proprioceptive, visual or auditory) contribute to the performance. Over the past few years, several studies have investigated the role of visual feedback in motor learning, yet evidence remains conflicting. The aim of this study was therefore to investigate the role of online visual feedback (VFb) on the acquisition and retention stages of motor learning associated with training in a reaching task. Thirty healthy subjects made ballistic reaching movements with their dominant arm toward two targets, on 2 consecutive days using a robotized exoskeleton (KINARM). They were randomly assigned to a group with (VFb) or without (NoVFb) VFb of index position during movement. On day 1, the task was performed before (baseline) and during the application of a velocity-dependent resistive force field (adaptation). To assess retention, participants repeated the task with the force field on day 2. Motor learning was characterized by: (1) the final endpoint error (movement accuracy) and (2) the initial angle (iANG) of deviation (motor planning). Even though both groups showed motor adaptation, the NoVFb-group exhibited slower learning and higher final endpoint error than the VFb-group. In some condition, subjects trained without visual feedback used more curved initial trajectories to anticipate for the perturbation. This observation suggests that learning to reach targets in a velocity-dependent resistive force field is possible even when feedback is limited. However, the absence of VFb leads to different strategies that were only apparent when reaching toward the most challenging target.

  12. Molecular Mechanics (MM) Force Fields for Modelling of Copper(II) Amino Acid Complexes in Different Environments

    Science.gov (United States)

    Sabolović, Jasmina

    2009-03-01

    New MM force field developed for modelling the properties of copper(II) complexes with aliphatic amino acid in vacuo, in crystal, and in aqueous solution was applied to study conformational properties of bis(N,N-diethylglycinato)copper(II). Two hypotheses are examined and confirmed as true: (i) the conformations which do not allow apical coordination to the copper(II) are the most stable in vacuo and in aqueous solution; (ii) MM calculations quantitatively support the supposition that the experimentally observed conformer is better suited for crystal packing than the in vacuo and in solution most stable conformers.

  13. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

    DEFF Research Database (Denmark)

    Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.

    2014-01-01

    . In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Moller-Plesset perturbation theory (MP2), and (3...... one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM)....

  14. Modelling of Ion Transport in Solids with a General Bond Valence Based Force-Field

    OpenAIRE

    Adams, S.; R.P. Rao

    2010-01-01

    Empirical bond length - bond valence relations provide insight into the link between structure of and ion transport in solid electrolytes. Building on our earlier systematic adjustment of bond valence (BV) parameters to the bond softness, here we discuss how the squared BV mismatch can be linked to the absolute energy scale and used as a general Morse-type interaction potential for analyzing low-energy pathways in ion conducting solid or mixed conductors either by an energy landscape approach...

  15. Fast Atomic Charge Calculation for Implementation into a Polarizable Force Field and Application to an Ion Channel Protein

    Directory of Open Access Journals (Sweden)

    Raiker Witter

    2015-01-01

    Full Text Available Polarization of atoms plays a substantial role in molecular interactions. Class I and II force fields mostly calculate with fixed atomic charges which can cause inadequate descriptions for highly charged molecules, for example, ion channels or metalloproteins. Changes in charge distributions can be included into molecular mechanics calculations by various methods. Here, we present a very fast computational quantum mechanical method, the Bond Polarization Theory (BPT. Atomic charges are obtained via a charge calculation method that depend on the 3D structure of the system in a similar way as atomic charges of ab initio calculations. Different methods of population analysis and charge calculation methods and their dependence on the basis set were investigated. A refined parameterization yielded excellent correlation of R=0.9967. The method was implemented in the force field COSMOS-NMR and applied to the histidine-tryptophan-complex of the transmembrane domain of the M2 protein channel of influenza A virus. Our calculations show that moderate changes of side chain torsion angle χ1 and small variations of χ2 of Trp-41 are necessary to switch from the inactivated into the activated state; and a rough two-side jump model of His-37 is supported for proton gating in accordance with a flipping mechanism.

  16. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field

    Science.gov (United States)

    Dziedzic, Jacek; Mao, Yuezhi; Shao, Yihan; Ponder, Jay; Head-Gordon, Teresa; Head-Gordon, Martin; Skylaris, Chris-Kriton

    2016-09-01

    We present a novel quantum mechanical/molecular mechanics (QM/MM) approach in which a quantum subsystem is coupled to a classical subsystem described by the AMOEBA polarizable force field. Our approach permits mutual polarization between the QM and MM subsystems, effected through multipolar electrostatics. Self-consistency is achieved for both the QM and MM subsystems through a total energy minimization scheme. We provide an expression for the Hamiltonian of the coupled QM/MM system, which we minimize using gradient methods. The QM subsystem is described by the onetep linear-scaling DFT approach, which makes use of strictly localized orbitals expressed in a set of periodic sinc basis functions equivalent to plane waves. The MM subsystem is described by the multipolar, polarizable force field AMOEBA, as implemented in tinker. Distributed multipole analysis is used to obtain, on the fly, a classical representation of the QM subsystem in terms of atom-centered multipoles. This auxiliary representation is used for all polarization interactions between QM and MM, allowing us to treat them on the same footing as in AMOEBA. We validate our method in tests of solute-solvent interaction energies, for neutral and charged molecules, demonstrating the simultaneous optimization of the quantum and classical degrees of freedom. Encouragingly, we find that the inclusion of explicit polarization in the MM part of QM/MM improves the agreement with fully QM calculations.

  17. Molecular simulation of caloric properties of fluids modelled by force fields with intramolecular contributions: Application to heat capacities

    Science.gov (United States)

    Smith, William R.; Jirsák, Jan; Nezbeda, Ivo; Qi, Weikai

    2017-07-01

    The calculation of caloric properties such as heat capacity, Joule-Thomson coefficients, and the speed of sound by classical force-field-based molecular simulation methodology has received scant attention in the literature, particularly for systems composed of complex molecules whose force fields (FFs) are characterized by a combination of intramolecular and intermolecular terms. The calculation of a thermodynamic property for a system whose molecules are described by such a FF involves the calculation of the residual property prior to its addition to the corresponding ideal-gas property, the latter of which is separately calculated, either using thermochemical compilations or nowadays accurate quantum mechanical calculations. Although the simulation of a volumetric residual property proceeds by simply replacing the intermolecular FF in the rigid molecule case by the total (intramolecular plus intermolecular) FF, this is not the case for a caloric property. We describe the correct methodology required to perform such calculations and illustrate it in this paper for the case of the internal energy and the enthalpy and their corresponding molar heat capacities. We provide numerical results for cP, one of the most important caloric properties. We also consider approximations to the correct calculation procedure previously used in the literature and illustrate their consequences for the examples of the relatively simple molecule 2-propanol, CH3CH(OH)CH3, and for the more complex molecule monoethanolamine, HO(CH2)2NH2, an important fluid used in carbon capture.

  18. Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods.

    Science.gov (United States)

    Broo, Anders; Nilsson Lill, Sten O

    2016-08-01

    A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.

  19. Force fields for simulating the interaction of surfaces with biological molecules

    Science.gov (United States)

    Martin, Lewis; Bilek, Marcela M.; Weiss, Anthony S.; Kuyucak, Serdar

    2016-01-01

    The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide–surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data. PMID:26855748

  20. A coarse-grained protein force field for folding and structure prediction.

    Science.gov (United States)

    Maupetit, Julien; Tuffery, P; Derreumaux, Philippe

    2007-11-01

    We have revisited the protein coarse-grained optimized potential for efficient structure prediction (OPEP). The training and validation sets consist of 13 and 16 protein targets. Because optimization depends on details of how the ensemble of decoys is sampled, trial conformations are generated by molecular dynamics, threading, greedy, and Monte Carlo simulations, or taken from publicly available databases. The OPEP parameters are varied by a genetic algorithm using a scoring function which requires that the native structure has the lowest energy, and the native-like structures have energy higher than the native structure but lower than the remote conformations. Overall, we find that OPEP correctly identifies 24 native or native-like states for 29 targets and has very similar capability to the all-atom discrete optimized protein energy model (DOPE), found recently to outperform five currently used energy models.

  1. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

    Science.gov (United States)

    Havrila, Marek; Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Krepl, Miroslav; Otyepka, Michal; Šponer, Jiří

    2015-12-10

    We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.

  2. A general intermolecular force field based on tight-binding quantum chemical calculations

    Science.gov (United States)

    Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

    2017-10-01

    A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

  3. Relativistic Force Field: Parametrization of (13)C-(1)H Nuclear Spin-Spin Coupling Constants.

    Science.gov (United States)

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-11-01

    Previously, we reported a reliable DU8 method for natural bond orbital (NBO)-aided parametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. As sophisticated NMR experiments for precise measurements of carbon-proton SSCCs are becoming more user-friendly and broadly utilized by the organic chemistry community to guide and inform the process of structure determination of complex organic compounds, we have now developed a fast and accurate method for computing (13)C-(1)H SSCCs. Fermi contacts computed with the DU8 basis set are scaled using selected NBO parameters in conjunction with empirical scaling coefficients. The method is optimized for inexpensive B3LYP/6-31G(d) geometries. The parametric scaling is based on a carefully selected training set of 274 ((3)J), 193 ((2)J), and 143 ((1)J) experimental (13)C-(1)H spin-spin coupling constants reported in the literature. The DU8 basis set, optimized for computing Fermi contacts, which by design had evolved from optimization of a collection of inexpensive 3-21G*, 4-21G, and 6-31G(d) bases, offers very short computational (wall) times even for relatively large organic molecules containing 15-20 carbon atoms. The most informative SSCCs for structure determination, i.e., (3)J, were computed with an accuracy of 0.41 Hz (rmsd). The new unified approach for computing (1)H-(1)H and (13)C-(1)H SSCCs is termed "DU8c".

  4. The coarse-grained OPEP force field for non-amyloid and amyloid proteins.

    Science.gov (United States)

    Chebaro, Yassmine; Pasquali, Samuela; Derreumaux, Philippe

    2012-08-02

    Coarse-grained protein models with various levels of granularity and degrees of freedom offer the possibility to explore many phenomena including folding, assembly, and recognition in terms of dynamics and thermodynamics that are inaccessible to all-atom representations in explicit aqueous solution. Here, we present a refined version of the coarse-grained optimized potential for efficient protein structure prediction (OPEP) based on a six-bead representation. The OPEP version 4.0 parameter set, which uses a new analytical formulation for the nonbonded interactions and adds specific side-chain-side-chain interactions for α-helix, is subjected to three tests. First, we show that molecular dynamics simulations at 300 K preserve the experimental rigid conformations of 17 proteins with 37-152 amino acids within a root-mean-square deviation (RMSD) of 3.1 Å after 30 ns. Extending the simulation time to 100 ns for five proteins does not change the RMSDs. Second, replica exchange molecular dynamics (REMD) simulations recover the NMR structures of three prototypical β-hairpin and α-helix peptides and the NMR three-stranded β-sheet topology of a 37-residue WW domain, starting from randomly chosen states. Third, REMD simulations on the ccβ peptide show a temperature transition from a three-stranded coiled coil to amyloid-like aggregates consistent with experiments, while simulations on low molecular weight aggregates of the prion protein helix 1 do not. Overall, these studies indicate the effectiveness of our OPEP4 coarse-grained model for protein folding and aggregation, and report two future directions for improvement.

  5. Assessment of Some Density Functional Theory Methods and Force Field Models in Describing Various Interaction Modes of Benzene Dimer

    Institute of Scientific and Technical Information of China (English)

    Yu-wei Zhou; Igor Ying Zhang; Jian-ming Wu; An-an Wu; Xin Xu

    2011-01-01

    Benzene dimer (bz2) is the simplest prototype of the π-π interactions.Such interactions are ubiquitous in diverse areas of science and molecular engineering.In the present work,we have made assessment on some modern density functional methods including B97-D,BLYP-D3,M06-2X,XYG3,and force field models including CHARMM,AMBER,MM3,AMOEBA on six important interaction modes of bz2.Our results not only highlight the usefulness of these cost-effective methods,which can be used as economic substitutes of the expensive CCSD(T) for complex real-world systems,but also indicate their weakness in the description of the π-π interactions,which points to the future direction for further improvements.

  6. Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

    Institute of Scientific and Technical Information of China (English)

    YAN XiuFen; JIANG Nan; MA Jing

    2009-01-01

    A series of theoretical approaches,including conventional FF03 and FF03-based polarization model,as well as the generalized energy-based fragmentation (GEBF) quantum chemistry method,have been applied to investigate the interactions between acetate ion (CH_3COO~-) and the α-subunit of human adult hemoglobin (designated as Hb-α) at four binding sites (Lys16,Lys90,Arg92,and Lys127),respectively.The FF03-based polarizable force fields show that the interaction energies between the CH_3COO~-group and Hb-α follow the trend of Arg92>Lys127>Lys90>Lys16.The complexation of CH_3COO~-with Hb-α is governed by the long-range electrostatic interactions and steric effect.

  7. Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A series of theoretical approaches,including conventional FF03 and FF03-based polarization model,as well as the generalized energy-based fragmentation(GEBF) quantum chemistry method,have been applied to investigate the interactions between acetate ion(CH3COO-) and the α-subunit of human adult hemoglobin(designated as Hb-α) at four binding sites(Lys16,Lys90,Arg92,and Lys127),respectively.The FF03-based polarizable force fields show that the interaction energies between the CH3COO-group and Hb-α follow the trend of Arg92>Lys127>Lys90>Lys16.The complexation of CH3COO-with Hb-α is governed by the long-range electrostatic interactions and steric effect.

  8. Study of deformation of droplet in external force field by using liquid-gas model of lattice-gas

    Energy Technology Data Exchange (ETDEWEB)

    Ebihara, Ken-ichi; Watanabe, Tadashi [Japan Atomic Energy Research Inst., Center for Promotion of Computational Science and Engineering, Tokai, Ibaraki (Japan)

    2000-10-01

    The deformation of the droplet by the external force which is assumed to be gravity is studied by using the liquid-gas model of lattice-gas. Two types of liquid-gas models, one is the minimal model and the other is the maximal model, which are distinguished from each other by the added long-range interactions are used for the simulation of the droplet deformation. The difference of the droplet deformation between the maximal model and the minimal model was observed. While the droplet of the minimal model elongates in the direction of the external force, the droplet of the maximal model elongates in the perpendicular direction to the external force. Therefore the droplet deformation in the external force field of the maximal model is more similar to the droplet deformation which is observed in experiments than that of the minimal model. (author)

  9. Can simulations quantitatively predict peptide transfer free energies to urea solutions? Thermodynamic concepts and force field limitations.

    Science.gov (United States)

    Horinek, Dominik; Netz, Roland R

    2011-06-16

    Many proteins denature when they are transferred to concentrated urea solutions. Three mechanisms for urea's denaturing ability have been proposed: (i) direct binding to polar parts of the protein surface, (ii) direct binding to nonpolar parts of the protein surface, and (iii) an indirect effect mediated by modifications of the bulk water properties. The disentanglement of these three processes has been the goal of many experimental and computational studies, yet there is no final agreement on the relative importance of the three contributions. The separation of the two direct mechanisms, albeit conceptually clear, is difficult in experimental studies and in simulations depends subtly on how the discrimination between polar and nonpolar groups is accomplished. Indirect effects, embodied in the change of solution activity as urea is added, are rarely monitored in urea/peptide simulations and thus have remained elusive in numerical studies. In this paper we establish a rigorous separation of all three contributions to the solvation thermodynamics of stretched peptide chains. We contrast this scenario with two commonly used model systems: the air/water interface and the interface between water and a hydrophobic alkane self-assembled monolayer. Together with bulk thermodynamic properties of urea/water mixed solvents, a complete thermodynamic description of the urea/water/peptide system is obtained: urea avoids the air/water interface but readily adsorbs at the oil-water interface and at hydrophobic as well as hydrophilic peptide chains, in accordance with experimental results. Simple thermodynamic arguments show that the indirect contribution to urea's denaturing capability is negligibly small, although urea strongly changes the water bulk properties as judged by the number of hydrogen bonds formed. Urea's tendency to bind to proteins is correctly reproduced with several force field combinations, but the quantitative binding strength as well as the relative importance

  10. Using an electrohydraulic ankle foot orthosis to study modifications in feedforward control during locomotor adaptation to force fields applied in stance

    Directory of Open Access Journals (Sweden)

    Bouyer Laurent J

    2009-06-01

    Full Text Available Abstract Background Adapting to external forces during walking has been proposed as a tool to improve locomotion after central nervous system injury. However, sensorimotor integration during walking varies according to the timing in the gait cycle, suggesting that adaptation may also depend on gait phases. In this study, an ElectroHydraulic AFO (EHO was used to apply forces specifically during mid-stance and push-off to evaluate if feedforward movement control can be adapted in these 2 gait phases. Methods Eleven healthy subjects walked on a treadmill before (3 min, during (5 min and after (5 min exposure to 2 force fields applied by the EHO (mid-stance/push-off; ~10 Nm, towards dorsiflexion. To evaluate modifications in feedforward control, strides with no force field ('catch strides' were unexpectedly inserted during the force field walking period. Results When initially exposed to a mid-stance force field (FF20%, subjects showed a significant increase in ankle dorsiflexion velocity. Catches applied early into the FF20% were similar to baseline (P > 0.99. Subjects gradually adapted by returning ankle velocity to baseline over ~50 strides. Catches applied thereafter showed decreased ankle velocity where the force field was normally applied, indicating the presence of feedforward adaptation. When initially exposed to a push-off force field (FF50%, plantarflexion velocity was reduced in the zone of force field application. No adaptation occurred over the 5 min exposure. Catch strides kinematics remained similar to control at all times, suggesting no feedforward adaptation. As a control, force fields assisting plantarflexion (-3.5 to -9.5 Nm were applied and increased ankle plantarflexion during push-off, confirming that the lack of kinematic changes during FF50% catch strides were not simply due to a large ankle impedance. Conclusion Together these results show that ankle exoskeletons such as the EHO can be used to study phase-specific adaptive

  11. Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Weimin; Niu, Haitao; Lin, Tong; Wang, Xungai; Kong, Lingxue [Institute for Frontier Materials, Deakin University, Waurn Ponds VIC 3216 (Australia)

    2014-01-28

    The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform external electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.

  12. Quartic force fields for excited electronic states: rovibronic reference data for the 1 (2)A' and 1 (2)A″ states of the isoformyl radical, HOC.

    Science.gov (United States)

    Morgan, W James; Fortenberry, Ryan C

    2015-01-25

    Quartic force fields (QFFs) have been shown to be an effective, accurate, and relatively compact means of computing rovibrational spectroscopic data for numerous molecules with numerous applications. However, excited states have been nearly excluded from the this approach since most accurate QFFs are based on the "gold standard" coupled cluster singles, doubles, and perturbative triples [CCSD(T)] method which is not readily extended to excited states. In this work, rovibronic spectroscopic data is provided for the isoformyl radical, a molecule of significance in combustion and astrochemistry, both through the traditional means of variational access to excited states with CCSD(T) and in the novel extension of QFFs routinely to treat electronically excited states through the standard coupled cluster excited state approach, equation of motion (EOM) CCSD. It is shown here that the new EOM-based QFF provides structural parameters and rotational constants that are quite close to those from a related CCSD(T)-based QFF for the 1 (2)A(″) excited state of HOC. The anharmonic vibrational frequency percent differences between the two QFFs are less than 0.4% for the O-H stretch, less than 1.9% for the C-O stretch, and around 3.0% for the bend. Even so, the pure excited state EOM-QFF anharmonic frequencies are still very good abinitio representations that may be applied to systems where electronically excited states are not variationally accessible. Additionally, rovibrational spectroscopic data is provided for the 1 (2)A(') ground state of HOC and for both the ground and excited state of DOC.

  13. Explicit treatment of hydrogen bonds in the universal force field: Validation and application for metal-organic frameworks, hydrates, and host-guest complexes

    Science.gov (United States)

    Coupry, Damien E.; Addicoat, Matthew A.; Heine, Thomas

    2017-10-01

    A straightforward means to include explicit hydrogen bonds within the Universal Force Field (UFF) is presented. Instead of treating hydrogen bonds as non-bonded interaction subjected to electrostatic and Lennard-Jones potentials, we introduce an explicit bond with a negligible bond order, thus maintaining the structural integrity of the H-bonded complexes and avoiding the necessity to assign arbitrary charges to the system. The explicit hydrogen bond changes the coordination number of the acceptor site and the approach is thus most suitable for systems with under-coordinated atoms, such as many metal-organic frameworks; however, it also shows an excellent performance for other systems involving a hydrogen-bonded framework. In particular, it is an excellent means for creating starting structures for molecular dynamics and for investigations employing more sophisticated methods. The approach is validated for the hydrogen bonded complexes in the S22 dataset and then employed for a set of metal-organic frameworks from the Computation-Ready Experimental database and several hydrogen bonded crystals including water ice and clathrates. We show that the direct inclusion of hydrogen bonds reduces the maximum error in predicted cell parameters from 66% to only 14%, and the mean unsigned error is similarly reduced from 14% to only 4%. We posit that with the inclusion of hydrogen bonding, the solvent-mediated breathing of frameworks such as MIL-53 is now accessible to rapid UFF calculations, which will further the aim of rapid computational scanning of metal-organic frameworks while providing better starting points for electronic structure calculations.

  14. Development of a reaxff reactive force field for silicon/oxygen/hydrogen/fluoride interactions and applications to hydroxylation and friction

    Science.gov (United States)

    Yeon, Jejoon

    Molecular dynamics (MD) simulations with the ReaxFF reactive force field were carried out to find the atomistic mechanisms for tribo-chemical reactions occurring at the sliding interface of fully-hydroxylated amorphous silica and oxidized silicon as a function of interfacial water amount. The ReaxFF-MD simulations showed a significant amount of mass transfer across the interface occurs during the sliding. In the absence of water molecules, the interfacial mixing was initiated by dehydroxylation followed by the Si-O-Si bond formation bridging two solid surfaces. In the presence of sub-monolayer thick water, the dissociation of water molecules can provide additional reaction pathways to form the Si-O-Si bridge bonds and mass transfers across the interface. However, when the amount of interfacial water molecules was large enough to form full monolayer, the degree of mass transfer was substantially reduced since the silicon atoms at the sliding interface were terminated with hydroxyl groups rather than forming interfacial Si-O-Si bridge bonds. The ReaxFF-MD simulations clearly showed the role of water molecules in atomic scale mechano-chemical processes during the sliding and provided physical insights into tribochemical wear processes of silicon oxide surfaces observed experimentally. In addition to this, we performed reactive force field molecular dynamics simulation to observe the hydrolysis reactions between water molecules and locally strained SiO2 geometries. We improved the Si/O/H force field from Fogarty et al.1, to more accurately describe the hydroxylation reaction barrier for strained and non-strained Si-O structures, which are about 20 kcal/mol and 30 kcal/mol, respectively. After optimization, energy barrier for the hydroxylation shows a good agreement with DFT data. The observation of silanol formation at the high-strain region of a silica nano-rod also supports the concept that the adsorption of water molecule: hydroxyl formation favors the geometry with

  15. The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Neumann, Marcus A.; van de Streek, Jacco

    2017-01-01

    Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance...... cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more...

  16. Highly Accurate Quartic Force Fields, Vibrational Frequencies, and Spectroscopic Constants for Cyclic and Linear C3H3(+)

    Science.gov (United States)

    Huang, Xinchuan; Taylor, Peter R.; Lee, Timothy J.

    2011-01-01

    High levels of theory have been used to compute quartic force fields (QFFs) for the cyclic and linear forms of the C H + molecular cation, referred to as c-C H + and I-C H +. Specifically the 33 3333 singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations, CCSD(T), has been used in conjunction with extrapolation to the one-particle basis set limit and corrections for scalar relativity and core correlation have been included. The QFFs have been used to compute highly accurate fundamental vibrational frequencies and other spectroscopic constants using both vibrational 2nd-order perturbation theory and variational methods to solve the nuclear Schroedinger equation. Agreement between our best computed fundamental vibrational frequencies and recent infrared photodissociation experiments is reasonable for most bands, but there are a few exceptions. Possible sources for the discrepancies are discussed. We determine the energy difference between the cyclic and linear forms of C H +, 33 obtaining 27.9 kcal/mol at 0 K, which should be the most reliable available. It is expected that the fundamental vibrational frequencies and spectroscopic constants presented here for c-C H + 33 and I-C H + are the most reliable available for the free gas-phase species and it is hoped that 33 these will be useful in the assignment of future high-resolution laboratory experiments or astronomical observations.

  17. raaSAFT: A framework enabling coarse-grained molecular dynamics simulations based on the SAFT- γ Mie force field

    Science.gov (United States)

    Ervik, Åsmund; Serratos, Guadalupe Jiménez; Müller, Erich A.

    2017-03-01

    We describe here raaSAFT, a Python code that enables the setup and running of coarse-grained molecular dynamics simulations in a systematic and efficient manner. The code is built on top of the popular HOOMD-blue code, and as such harnesses the computational power of GPUs. The methodology makes use of the SAFT- γ Mie force field, so the resulting coarse grained pair potentials are both closely linked to and consistent with the macroscopic thermodynamic properties of the simulated fluid. In raaSAFT both homonuclear and heteronuclear models are implemented for a wide range of compounds spanning from linear alkanes, to more complicated fluids such as water and alcohols, all the way up to nonionic surfactants and models of asphaltenes and resins. Adding new compounds as well as new features is made straightforward by the modularity of the code. To demonstrate the ease-of-use of raaSAFT, we give a detailed walkthrough of how to simulate liquid-liquid equilibrium of a hydrocarbon with water. We describe in detail how both homonuclear and heteronuclear compounds are implemented. To demonstrate the performance and versatility of raaSAFT, we simulate a large polymer-solvent mixture with 300 polystyrene molecules dissolved in 42 700 molecules of heptane, reproducing the experimentally observed temperature-dependent solubility of polystyrene. For this case we obtain a speedup of more than three orders of magnitude as compared to atomistically-detailed simulations.

  18. A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

    Science.gov (United States)

    Biswas, P K; Gogonea, Valentin

    2008-10-21

    We present an ab initio polarizable representation of classical molecular mechanics (MM) atoms by employing an angular momentum-based expansion scheme of the point charges into partial wave orbitals. The charge density represented by these orbitals can be fully polarized, and for hybrid quantum-mechanical-molecular-mechanical (QM/MM) calculations, mutual polarization within the QM/MM Hamiltonian can be obtained. We present the mathematical formulation and the analytical expressions for the energy and forces pertaining to the method. We further develop a variational scheme to appropriately determine the expansion coefficients and then validate the method by considering polarizations of ions by the QM system employing the hybrid GROMACS-CPMD QM/MM program. Finally, we present a simpler prescription for adding isotropic polarizability to MM atoms in a QM/MM simulation. Employing this simpler scheme, we present QM/MM energy minimization results for the classic case of a water dimer and a hydrogen sulfide dimer. Also, we present single-point QM/MM results with and without the polarization to study the change in the ionization potential of tetrahydrobiopterin (BH(4)) in water and the change in the interaction energy of solvated BH(4) (described by MM) with the P(450) heme described by QM. The model can be employed for the development of an extensive classical polarizable force-field.

  19. Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field

    Science.gov (United States)

    Kalimeri, Maria; Derreumaux, Philippe; Sterpone, Fabio

    2017-01-01

    We present the first investigation of the kinetic and thermodynamic stability of two homologous thermophilic and mesophilic proteins based on the coarse-grained model OPEP. The object of our investigation is a pair of G-domains of relatively large size, 200 amino acids each, with an experimental stability gap of about 40 K. The OPEP force field is able to maintain stable the fold of these relatively large proteins within the hundrend-nanosecond time scale without including external constraints. This makes possible to characterize the conformational landscape of the folded protein as well as to explore the unfolding. In agreement with all-atom simulations used as a reference, we show that the conformational landscape of the thermophilic protein is characterized by a larger number of substates with slower dynamics on the network of states and more resilient to temperature increase. Moreover, we verify the stability gap between the two proteins using replica-exchange simulations and estimate a difference between the melting temperatures of about 23 K, in fair agreement with experiment. The detailed investigation of the unfolding thermodynamics, allows to gain insight into the mechanism underlying the enhanced stability of the thermophile relating it to a smaller heat capacity of unfolding.

  20. Development of the ReaxFFCBN reactive force field for the improved design of liquid CBN hydrogen storage materials.

    Science.gov (United States)

    Pai, Sung Jin; Yeo, Byung Chul; Han, Sang Soo

    2016-01-21

    Liquid CBN (carbon-boron-nitrogen) hydrogen-storage materials such as 3-methyl-1,2-BN-cyclopentane have the advantage of being easily accessible for use in current liquid-fuel infrastructure. To develop practical liquid CBN hydrogen-storage materials, it is of great importance to understand the reaction pathways of hydrogenation/dehydrogenation in the liquid phase, which are difficult to discover by experimental methods. Herein, we developed a reactive force field (ReaxFFCBN) from quantum mechanical (QM) calculations based on density functional theory for the storage of hydrogen in BN-substituted cyclic hydrocarbon materials. The developed ReaxFFCBN provides similar dehydrogenation pathways and energetics to those predicted by QM calculations. Moreover, molecular dynamics (MD) simulations with the developed ReaxFFCBN can predict the stability and dehydrogenation behavior of various liquid CBN hydrogen-storage materials. Our simulations reveal that a unimolecular dehydrogenation mechanism is preferred in liquid CBN hydrogen-storage materials. However, as the temperature in the simulation increases, the contribution of a bimolecular dehydrogenation mechanism also increases. Moreover, our ReaxFF MD simulations show that in terms of thermal stability and dehydrogenation kinetics, liquid CBN materials with a hexagonal structure are more suitable materials than those with a pentagonal structure. We expect that the developed ReaxFFCBN could be a useful protocol in developing novel liquid CBN hydrogen-storage materials.

  1. A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

    Science.gov (United States)

    Michalowsky, Julian; Schäfer, Lars V.; Holm, Christian; Smiatek, Jens

    2017-02-01

    We present a refined version of the polarizable Martini water model - coined refPOL - designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water force field when particle mesh Ewald electrostatics are employed. Our study reveals that the model remains applicable with various commonly used settings for the non-bonded interactions, including reaction field electrostatics. The oil/water partitioning behavior of uncharged Martini bead types is thoroughly investigated: Lennard-Jones interactions between the refPOL model and the remaining Martini beads are adjusted to reproduce the hydration free energies obtained with the original polarizable water model, while free energies of solvation in apolar media remain unchanged. The cross-interactions with charged bead types are parameterized to agree with the experimentally observed area per lipid of a fully solvated dipalmitoylphosphatidylcholine bilayer. We additionally verify the model by analyzing the potentials of mean force between different sample pairs in refPOL water and comparing the results to reference data obtained using the original polarizable Martini water model as well as fully atomistic simulations. Based on the results, we suggest to replace the original polarizable Martini water model with the new refPOL model for future applications.

  2. Electro-hydrodynamic force field and flow patterns generated by a DC corona discharge in the air

    Science.gov (United States)

    Monrolin, Nicolas; Plouraboue, Franck; Praud, Olivier

    2016-11-01

    Ionic wind refers to the electro-convection of ionised air between high voltage electrodes. Microscopic ion-neutral collisions are responsible for momentum transfer from accelerated ions, subjected to the electric field, to the neutral gas molecules resulting in a macroscopic airflow acceleration. In the past decades it has been investigated for various purposes from food drying through aerodynamic flow control and eventually laptop cooling. One consequence of air acceleration between the electrodes is thrust generation, often referred to as the Biefeld-Brown effect or electro-hydrodynamic thrust. In this experimental study, the ionic wind velocity field is measured with the PIV method. From computing the acceleration of the air we work out the electrostatic force field for various electrodes configurations. This enables an original direct evaluation of the force distribution as well as the influence of electrodes shape and position. Thrust computation based on the flow acceleration are compared with digital scale measurements. Complex flow features are highlighted such as vortex shedding, indicating that aerodynamic effects may play a significant role. Furthermore, the aerodynamic drag force exerted on the electrodes is quantified by choosing an appropriate control volume. Authors thank Region Midi-Pyrenee and CNES Launcher Directorate for financial support.

  3. Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields

    Science.gov (United States)

    Kamath, Ganesh; Kurnikov, Igor; Fain, Boris; Leontyev, Igor; Illarionov, Alexey; Butin, Oleg; Olevanov, Michael; Pereyaslavets, Leonid

    2016-11-01

    We present the performance of blind predictions of water—cyclohexane distribution coefficients for 53 drug-like compounds in the SAMPL5 challenge by three methods currently in use within our group. Two of them utilize QMPFF3 and ARROW, polarizable force-fields of varying complexity, and the third uses the General Amber Force-Field (GAFF). The polarizable FF's are implemented in an in-house MD package, Arbalest. We find that when we had time to parametrize the functional groups with care (batch 0), the polarizable force-fields outperformed the non-polarizable one. Conversely, on the full set of 53 compounds, GAFF performed better than both QMPFF3 and ARROW. We also describe the torsion-restrain method we used to improve sampling of molecular conformational space and thus the overall accuracy of prediction. The SAMPL5 challenge highlighted several drawbacks of our force-fields, such as our significant systematic over-estimation of hydrophobic interactions, specifically for alkanes and aromatic rings.

  4. The effect of force feedback delay on stiffness perception and grip force modulation during tool-mediated interaction with elastic force fields.

    Science.gov (United States)

    Leib, Raz; Karniel, Amir; Nisky, Ilana

    2015-05-01

    During interaction with objects, we form an internal representation of their mechanical properties. This representation is used for perception and for guiding actions, such as in precision grip, where grip force is modulated with the predicted load forces. In this study, we explored the relationship between grip force adjustment and perception of stiffness during interaction with linear elastic force fields. In a forced-choice paradigm, participants probed pairs of virtual force fields while grasping a force sensor that was attached to a haptic device. For each pair, they were asked which field had higher level of stiffness. In half of the pairs, the force feedback of one of the fields was delayed. Participants underestimated the stiffness of the delayed field relatively to the nondelayed, but their grip force characteristics were similar in both conditions. We analyzed the magnitude of the grip force and the lag between the grip force and the load force in the exploratory probing movements within each trial. Right before answering which force field had higher level of stiffness, both magnitude and lag were similar between delayed and nondelayed force fields. These results suggest that an accurate internal representation of environment stiffness and time delay was used for adjusting the grip force. However, this representation did not help in eliminating the bias in stiffness perception. We argue that during performance of a perceptual task that is based on proprioceptive feedback, separate neural mechanisms are responsible for perception and action-related computations in the brain.

  5. Enhanced crosslimb transfer of force-field learning for dynamics that are identical in extrinsic and joint-based coordinates for both limbs.

    Science.gov (United States)

    Carroll, Timothy J; de Rugy, Aymar; Howard, Ian S; Ingram, James N; Wolpert, Daniel M

    2016-01-01

    Humans are able to adapt their motor commands to make accurate movements in novel sensorimotor environments, such as when wielding tools that alter limb dynamics. However, it is unclear to what extent sensorimotor representations, obtained through experience with one limb, are available to the opposite, untrained limb and in which form they are available. Here, we compared crosslimb transfer of force-field compensation after participants adapted to a velocity-dependent curl field, oriented either in the sagittal or the transverse plane. Due to the mirror symmetry of the limbs, the force field had identical effects for both limbs in joint and extrinsic coordinates in the sagittal plane but conflicting joint-based effects in the transverse plane. The degree of force-field compensation exhibited by the opposite arm in probe trials immediately after initial learning was significantly greater after sagittal (26 ± 5%) than transverse plane adaptation (9 ± 4%; P coordinates for the two limbs. The data reveal that neural representations of novel dynamics are only partially available to the opposite limb, since transfer is incomplete even when force-field perturbation is spatially compatible for the two limbs, according to both intrinsic and extrinsic coordinates.

  6. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations.

    Science.gov (United States)

    Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea

    2012-05-08

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard.

  7. Structure of large nitrate-water clusters at ambient temperatures: simulations with effective fragment potentials and force fields with implications for atmospheric chemistry.

    Science.gov (United States)

    Miller, Yifat; Thomas, Jennie L; Kemp, Daniel D; Finlayson-Pitts, Barbara J; Gordon, Mark S; Tobias, Douglas J; Gerber, R Benny

    2009-11-19

    Structural properties of large NO(3)(-).(H(2)O)(n) (n = 15-500) clusters are studied by Monte Carlo simulations using effective fragment potentials (EFPs) and by classical molecular dynamics simulations using a polarizable empirical force field. The simulation results are analyzed with a focus on the description of hydrogen bonding and solvation in the clusters. In addition, a comparison between the electronic structure based EFP and the classical force field description of the 32 water cluster system is presented. The EFP simulations, which focused on the cases of n = 15 and 32, show an internal, fully solvated structure and a "surface adsorbed" structure for the 32 water cluster at 300 K, with the latter configuration being more probable. The internal solvated structure and the "surface adsorbed" structure differ considerably in their hydrogen bonding coordination numbers. The force field based simulations agree qualitatively with these results, and the local geometry of NO(3)(-) and solvation at the surface-adsorbed site in the force field simulations are similar to those predicted using EFPs. Differences and similarities between the description of hydrogen bonding of the anion in the two approaches are discussed. Extensive classical force field based simulations at 250 K predict that long time scale stability of "internal" NO(3)(-), which is characteristic of extended bulk aqueous interfaces, emerges only for n > 300. Ab initio Møller-Plesset perturbation theory is used to test the geometries of selected surface and interior anions for n = 32, and the results are compared to the EFP and MD simulations. Qualitatively, all approaches agree that surface structures are preferred over the interior structures for clusters of this size. The relatively large aqueous clusters of NO(3)(-) studied here are of comparable size to clusters that lead to new particle formation in air. Nitrate ions on the surface of such clusters may have significantly different photochemistry

  8. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Trondheim (Norway)

    2015-12-31

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

  9. Formation, characterization and dynamics of onion like carbon structures from nanodiamonds using reactive force-fields for electrical energy storage

    Energy Technology Data Exchange (ETDEWEB)

    Ganesh, Panchapakesan [ORNL; Kent, Paul R [ORNL; Mochalin, Vadym N [ORNL

    2011-01-01

    We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbon nanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbon nanostructure appears, with a shell-shell spacing of about {approx}3.4 {angstrom} for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large ({approx}29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.

  10. Formation, characterization, and dynamics of onion-like carbon structures for electrical energy storage from nanodiamonds using reactive force fields

    Energy Technology Data Exchange (ETDEWEB)

    Ganesh, P. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science; Kent, P. R. C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Science; Mochalin, V. [Drexel Univ., Philadelphia, PA (United States). Dept. of Materials Science and Engineering

    2011-10-01

    We simulate the experimentally observed graphitization of nanodiamonds into multi-shell onion-like carbonnanostructures, also called carbon onions, at different temperatures, using reactive force fields. The simulations include long-range Coulomb and van der Waals interactions. Our results suggest that long-range interactions play a crucial role in the phase-stability and the graphitization process. Graphitization is both enthalpically and entropically driven and can hence be controlled with temperature. The outer layers of the nanodiamond have a lower kinetic barrier toward graphitization irrespective of the size of the nanodiamond and graphitize within a few-hundred picoseconds, with a large volume increase. The inner core of the nanodiamonds displays a large size-dependent kinetic barrier, and graphitizes much more slowly with abrupt jumps in the internal energy. It eventually graphitizes by releasing pressure and expands once the outer shells have graphitized. The degree of transformation at a particular temperature is thereby determined by a delicate balance between the thermal energy, long-range interactions, and the entropic/enthalpic free energy gained by graphitization. Upon full graphitization, a multi-shell carbonnanostructure appears, with a shell-shell spacing of about ~3.4 Å for all sizes. The shells are highly defective with predominantly five- and seven-membered rings to curve space. Larger nanodiamonds with a diameter of 4 nm can graphitize into spiral structures with a large (~29-atom carbon ring) pore opening on the outermost shell. Such a large one-way channel is most attractive for a controlled insertion of molecules/ions such as Li ions, water, or ionic liquids, for increased electrochemical capacitor or battery electrode applications.

  11. Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.

    Science.gov (United States)

    Mao, Yuezhi; Demerdash, Omar; Head-Gordon, Martin; Head-Gordon, Teresa

    2016-11-08

    AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from

  12. Chemical Potentials, Activity Coefficients, and Solubility in Aqueous NaCl Solutions: Prediction by Polarizable Force Fields.

    Science.gov (United States)

    Moučka, Filip; Nezbeda, Ivo; Smith, William R

    2015-04-14

    We describe a computationally efficient molecular simulation methodology for calculating the concentration dependence of the chemical potentials of both solute and solvent in aqueous electrolyte solutions, based on simulations of the salt chemical potential alone. We use our approach to study the predictions for aqueous NaCl solutions at ambient conditions of these properties by the recently developed polarizable force fields (FFs) AH/BK3 of Kiss and Baranyai (J. Chem. Phys. 2013, 138, 204507) and AH/SWM4-DP of Lamoureux and Roux (J. Phys. Chem. B 2006, 110, 3308 - 3322) and by the nonpolarizable JC FF of Joung and Cheatham tailored to SPC/E water (J. Phys. Chem. B 2008, 112, 9020 - 9041). We also consider their predictions of the concentration dependence of the electrolyte activity coefficient, the crystalline solid chemical potential, the electrolyte solubility, and the solution specific volume. We first highlight the disagreement in the literature concerning calculations of solubility by means of molecular simulation in the case of the JC FF and provide strong evidence of the correctness of our methodology based on recent independently obtained results for this important test case. We then compare the predictions of the three FFs with each other and with experiment and draw conclusions concerning their relative merits, with particular emphasis on the salt chemical potential and activity coefficient vs concentration curves and their derivatives. The latter curves have only previously been available from Kirkwood-Buff integrals, which require approximate numerical integrations over system pair correlation functions at each concentration. Unlike the case of the other FFs, the AH/BK3 curves are nearly parallel to the corresponding experimental curves at moderate and higher concentrations. This leads to an excellent prediction of the water chemical potential via the Gibbs-Duhem equation and enables the activity coefficient curve to be brought into excellent agreement

  13. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

    Science.gov (United States)

    Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

    2017-02-14

    In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R(2) value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R(2) values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

  14. Infrared and Raman spectra of bicyclic molecules using scaled noncorrelated and correlated {ital ab initio} force fields

    Energy Technology Data Exchange (ETDEWEB)

    Collier, W.B. [Department of Chemistry, Oral Roberts University, Tulsa, Oklahoma 74171 (United States); Magdo, I. [Gedeon Richter Ltd., Molecular Design Unit, P.O. Box 27, H-1475, Budapest (Hungary); Klots, T.D. [Bartlesville Thermodynamic Group, BDM Petroleum Technologies, P.O. Box 2543, Bartlesville, Oklahoma 74005 (United States)

    1999-03-01

    This paper reports the application of a scaled {ital ab initio} calculated harmonic force field to predict the frequencies, infrared intensities, Raman intensities, and depolarization ratios of benzofuran, benzothiophene, indole, benzothiazole, and benzoxazole. The theoretical calculations were made using the Hartree{endash}Fock HF/3-21G{sup {asterisk}} and HF/6-31G{sup {asterisk}} basis sets and density-functional theory (DFT)B3-LYP/6-31G{sup {asterisk}} levels. The equilibrium calculated force constants are scaled according to the method of Pulay and compared with the experimentally determined frequencies, intensities, and depolarization ratios to assess the accuracy and fit of the theoretical calculation. Methods for quantitative comparison of intensities were developed. The double numerical differentiation algorithm of Komornicki and McIver was analyzed and used to calculate the Raman intensities for the (DFT)B3-LYP/6-31G{sup {asterisk}} model. The (DFT)B3-LYP/6-31G{sup {asterisk}} model is approaching the harmonic limit in the planar and nonplanar refinement of these bicyclics with wave number fits of 5 and 4 cm{sup {minus}1}, respectively. It reduces the need for scale factors and increases their transfer accuracy, largely because the scale factors values cluster near unity. The Komornicki and McIver algorithm is still a viable method for calculating Raman intensity information for methods that do not have analytic routines programmed. The main shortcoming to this method may lie in the tighter self-consistent field (SCF) convergence criterion possibly needed to calculate Raman intensities for the totally symmetric modes of large molecules. The (DFT)B3-LYP/6-31G{sup {asterisk}} model was superior for calculating the planar intensities, but equal to the HF methods for predicting the nonplanar intensities. {copyright} {ital 1999 American Institute of Physics.}

  15. Effect of tonic pain on motor acquisition and retention while learning to reach in a force field.

    Directory of Open Access Journals (Sweden)

    Mélanie Lamothe

    Full Text Available Most patients receiving intensive rehabilitation to improve their upper limb function experience pain. Despite this, the impact of pain on the ability to learn a specific motor task is still unknown. The aim of this study was to determine whether the presence of experimental tonic pain interferes with the acquisition and retention stages of motor learning associated with training in a reaching task. Twenty-nine healthy subjects were randomized to either a Control or Pain Group (receiving topical capsaicin cream on the upper arm during training on Day 1. On two consecutive days, subjects made ballistic movements towards two targets (NEAR/FAR using a robotized exoskeleton. On Day 1, the task was performed without (baseline and with a force field (adaptation. The adaptation task was repeated on Day 2. Task performance was assessed using index distance from the target at the end of the reaching movement. Motor planning was assessed using initial angle of deviation of index trajectory from a straight line to the target. Results show that tonic pain did not affect baseline reaching. Both groups improved task performance across time (p<0.001, but the Pain group showed a larger final error (under-compensation than the Control group for the FAR target (p = 0.030 during both acquisition and retention. Moreover, a Group x Time interaction (p = 0.028 was observed on initial angle of deviation, suggesting that subjects with Pain made larger adjustments in the feedforward component of the movement over time. Interestingly, behaviour of the Pain group was very stable from the end of Day 1 (with pain to the beginning of Day 2 (pain-free, indicating that the differences observed could not solely be explained by the impact of pain on immediate performance. This suggests that if people learn to move differently in the presence of pain, they might maintain this altered strategy over time.

  16. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations.

    Science.gov (United States)

    Ahlstrand, Emma; Hermansson, Kersti; Friedman, Ran

    2017-03-24

    Zinc plays important roles in structural stabilization of proteins, enzyme catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynamics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Drude polarizable force field agreed better with the ab initio results, although the deviations between QM and MM were still rather large (40-96 kcal/mol). In order to gain further insight into Zn-ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand-ligand interactions did not play a significant role in the binding of Zn. Finally, analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn binding dynamics. An exchange between carboxylate (Asp/Glu) and imidazole (His) is less likely.

  17. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    Science.gov (United States)

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz.

  18. Effects of temperature on the properties of glycerol: a computer simulation study of five different force fields.

    Science.gov (United States)

    Jahn, David A; Akinkunmi, Frederick O; Giovambattista, Nicolas

    2014-09-25

    We perform molecular dynamics simulations of glycerol (propane-1,2,3-triol) at normal pressure and a wide range of temperatures (300-460 K) and study the sensitivity of simulation results to the force field (FF) considered. We employ five commonly used FFs: (i) AMBER, (ii) CHARMM22, and (iii) three versions of the OPLS-AA FF (OPLS1, OPLS2, and OPLS3). We study thermodynamic (density ρ(T), thermal expansion coefficient αP(T), isobaric specific heat cP(T)), dynamic (diffusion coefficient D(T)), as well as structural properties (molecular conformations and hydrogen-bond statistics). In comparison with experiments, FFs i and iii provide reasonable estimations of ρ(T) with deviations of ≤4.5%; for FF ii, deviations in density are more pronounced, ≤9%. Values of αP(T) vary considerably among the FFs; e.g., deviations are ≤9% for OPLS1-FF and ≤60% for FF ii. For all models studied, values of cP(T) are approximately twice the corresponding experimental values. Diffusion coefficients are very sensitive to the FFs considered. Specifically, for FFs i and ii and OPLS3, the values of D(T) are remarkably close to the experimental values over the whole range of temperatures studied. Instead, in the cases of OPLS1 and OPLS2-FFs, D(T) is underestimated by approximately 2 orders of magnitude. Interestingly, in all cases, D(T) can be well described by a Vogel-Tamman-Fulcher equation, as observed in experiments. We present a detailed characterization of glycerol backbone conformation based on the traditional classification introduced by Bastiansen, defined in terms of glycerol's OCCC dihedral angles. All FFs indicate that the conformer population varies smoothly with temperature. However, the FFs provide very different conformer distributions. This implies that, from the microscopic point of view, these glycerol models may provide very different liquid environments for, for example, guest biomolecules and hence may play a relevant role in interpreting simulation results

  19. Solar wind ion impacts into ice surfaces: A molecular-dynamics study using the REAX force field

    Science.gov (United States)

    Anders, Christian; Urbassek, Herbert M.

    2017-01-01

    Molecular dynamics simulation is used to study the effects of solar-wind ion irradiation on an ice target, focusing on the effects of nuclear energy deposition. A reactive force field (REAX) interatomic interaction potential is employed that allows us to model the breaking and formation of molecular bonds and hence to follow the chemistry occurring in the target. As ions we study H and He ions as typical constituents of the solar wind, and Ne as an example of a heavier ion; they impact at the speed of maximum flux in the solar wind, 400 km/s. The ice consists of a mixture of H2O, CO2, CH3OH and NH3. We find that molecular dissociations occur within 0.2 ps after ion impact and new products are formed up to a time of 1 ps; only water has a slower dynamics, due to highly mobile H atoms allowing for late recombinations. The number of dissociations, and hence also of product molecules increases from H over He to Ne ion projectiles and can be quantified by the amount of energy deposited in the target by these ions. The most abundant products formed include CO, OH and NH2. Reaction products are most complex for Ne impact, and include H3O, formaldehyde (H2CO), HO2, and NO. Formaldehyde is important as it is formed relatively frequently and is known as a precursor in the formation of sugars. In addition, molecules containing all CHON elements are formed, among which are CH2NO, CONH, methanolamine (CH5NO), and ethyne (C2H2). Repeated impacts generate novel, and more complex product species; we found CN, CH4, CH3NO, methylamine (CH3NH2), and acetamide (CH3CONH2), among others; the complex species are formed less frequently than the simple fragments. Sputtering occurs for all projectiles, even H. The ejecta are either original molecules - in particular CO2 - or simple fragments; only few product molecules are emitted.

  20. Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22.

    Science.gov (United States)

    Olubiyi, Olujide O; Strodel, Birgit

    2016-12-01

    In this article we provide a data package containing the topology files and parameters compatible with the CHARMM22 force field for thirteen non-natural amino acids. The force field parameters were derived based on quantum mechanical (QM) calculations involving geometry optimization and potential energy surface scanning at the HF 6-31G(d) and HF 6-311G(d,p) levels of theory. The resulting energy data points were fitted to mathematical functions representing each component of the CHARMM22 force field. Further fine-tuning of the parameters utilized molecular mechanics energies, which were iteratively calculated and compared to the corresponding QM values until the latter were satisfactorily reproduced. The final force field data were validated with molecular dynamics simulations in explicit solvent conditions.

  1. Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22

    Directory of Open Access Journals (Sweden)

    Olujide O. Olubiyi

    2016-12-01

    Full Text Available In this article we provide a data package containing the topology files and parameters compatible with the CHARMM22 force field for thirteen non-natural amino acids. The force field parameters were derived based on quantum mechanical (QM calculations involving geometry optimization and potential energy surface scanning at the HF 6-31G(d and HF 6-311G(d,p levels of theory. The resulting energy data points were fitted to mathematical functions representing each component of the CHARMM22 force field. Further fine-tuning of the parameters utilized molecular mechanics energies, which were iteratively calculated and compared to the corresponding QM values until the latter were satisfactorily reproduced. The final force field data were validated with molecular dynamics simulations in explicit solvent conditions.

  2. Parameterizing complex reactive force fields using multiple objective evolutionary strategies (MOES): Part 2: transferability of ReaxFF models to C-H-N-O energetic materials.

    Science.gov (United States)

    Rice, Betsy M; Larentzos, James P; Byrd, Edward F C; Weingarten, N Scott

    2015-02-10

    The Multiple Objective Evolutionary Strategies (MOES) algorithm was used to parametrize force fields having the form of the reactive models ReaxFF (van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. J. Phys. Chem. A 2001, 105, 9396) and ReaxFF-lg (Liu, L.; Liu, Y.; Zybin, S. V.; Sun, H.; Goddard, W. A. J. Phys. Chem. A 2011, 115, 11016) in an attempt to produce equal or superior ambient state crystallographic structural results for cyclotrimethylene trinitramine (RDX). Promising candidates were then subjected to molecular dynamics simulations of five other well-known conventional energetic materials to assess the degree of transferability of the models. Two models generated through the MOES search were shown to have performance better than or as good as ReaxFF-lg in describing the six energetic systems modeled. This study shows that MOES is an effective and efficient method to develop complex force fields.

  3. In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2005-01-01

    We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

  4. The atlas of the diagrams for the generalization of the 4th Appelrot class of especially remarkable motions to a gyrostat in a double force field

    OpenAIRE

    Ryabov, Pavel E.; Smirnov, Gleb E.; Kharlamov, Mikhail P.

    2013-01-01

    For the system with two degrees of freedom, which is an analogue of the 4th Appelrot class for a gyrostat of the Kowalevski type in a double force field the problem of the classification of bifurcation diagrams is solved. The separating set is built and its completeness is proved. All transformations taking place in the diagrams are shown. The results serve as a necessary part of solving the problem of obtaining the topological invariants for the Reyman - Semenov-Tian-Shansky system.

  5. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

    Science.gov (United States)

    Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Cheatham, Thomas E; Galindo-Murillo, Rodrigo; Jurečka, Petr

    2015-12-01

    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

  6. Infrared spectra of CF(2)=CHD and CF(2)=CD(2): scaled quantum-chemical force fields and an equilibrium structure for 1,1-difluoroethylene.

    Science.gov (United States)

    McKean, Donald C; Law, Mark M; Groner, Peter; Conrad, Andrew R; Tubergen, Michael J; Feller, David; Moore, Michael C; Craig, Norman C

    2010-09-02

    Infrared (IR) spectra in the gas phase are reported for CF(2)=CHD and CF(2)=CD(2) in the region 350-4000 cm(-1). Ab initio calculations of an harmonic force-field and anharmonicity constants have been made with an MP2/aug-cc-pVTZ model. These enable a number of Fermi resonances in each species to be analyzed and a complete set of "observed" harmonic frequencies to be derived. The latter are combined with similar data for CF(2)=CH(2) in a scaling of the model harmonic force field to both anharmonic and harmonic frequencies. Inspection of the scale factors reveals minor defects of the model, evident in the out-of-plane wagging modes and in the CF stretch/CF stretch interaction force constant. Fermi resonance treatments involved in all isotopomers studied are compatible with the overall force-field refinement results. The treatment leaves a small anomaly in the (13)C shift on nu(1). Improved microwave spectra are reported for five isotopic species, and a semiexperimental equilibrium structure for F(2)C=CH(2) is determined and compared favorably with the structure obtained from new high-level ab initio calculations. Centrifugal distortion constants are predicted for the five isotopic species, and those for F(2)C=CH(2) are compared with values fit to microwave spectra.

  7. Absolute Free Energy of Binding and Entropy of the FKBP12-FK506 Complex: Effects of the Force Field.

    Science.gov (United States)

    General, Ignacio J; Meirovitch, Hagai

    2013-10-08

    The hypothetical scanning molecular dynamics (HSMD) method combined with thermodynamic integration (HSMD-TI) has been extended recently for calculating ΔA(0)-the absolute free energy of binding of a ligand to a protein. With HSMD-TI, ΔA(0) is obtained in a new way as a sum of several components, among them is ΔSligand-the change in the conformational entropy as the ligand is transferred from the bulk solvent to the active site-this entropy is obtained by a specific reconstruction procedure. This unique aspect of HSMD (which is useful in rational drug design) is in particular important for treating large ligands, where ΔSligand might be significant. Technically, one should verify that the results for ΔSligand converge-a property that might become more difficult for large ligands; therefore, studying ligands of increasing size would define the range of applicability of HSMD-TI for binding. In this paper, we check the performance of HSMD-TI by applying it to the relatively large ligand FK506 (126 atoms) complexed with the protein FKBP12, where ΔA(0) = -12.8 kcal/mol is known experimentally as well as the crystal structure of the complex. This structure was initially equilibrated by carrying out a 100 ns molecular dynamics trajectory, where the system is modeled by the AMBER force field, TIP3P water, and Particle Mesh Ewald. HSMD-TI calculations were carried out in three conformational regions defined by the intervals [0.2,2], [2,5], and [5,100] ns along the trajectory, where local equilibration of the total energy has been observed; we obtained ΔA(0) = -13.6 ± 1.1, -16.6 ± 1.4, and -16.7 ± 1.4 kcal/mol, respectively indicating the following: (1) The second and third regions belong to the same conformational subspace of the complex, which is different from the [0.2,2] ns subspace. (2) The unsatisfactory result for ΔA(0) obtained in the well equilibrated (hence theoretically preferred) latter regions reflects the nonperfect modeling used, which however (3

  8. The rotation-vibration structure of the SO2 C ˜ 1B2 state explained by a new internal coordinate force field

    Science.gov (United States)

    Jiang, Jun; Park, G. Barratt; Field, Robert W.

    2016-04-01

    A new quartic force field for the SO2 C ˜ 1B2 state has been derived, based on high resolution data from S16O2 and S18O2. Included are eight b2 symmetry vibrational levels of S16O2 reported in the first paper of this series [G. B. Park et al., J. Chem. Phys. 144, 144311 (2016)]. Many of the experimental observables not included in the fit, such as the Franck-Condon intensities and the Coriolis-perturbed effective C rotational constants of highly anharmonic C ˜ state vibrational levels, are well reproduced using our force field. Because the two stretching modes of the C ˜ state are strongly coupled via Fermi-133 interaction, the vibrational structure of the C ˜ state is analyzed in a Fermi-system basis set, constructed explicitly in this work via partial diagonalization of the vibrational Hamiltonian. The physical significance of the Fermi-system basis is discussed in terms of semiclassical dynamics, based on study of Fermi-resonance systems by Kellman and Xiao [J. Chem. Phys. 93, 5821 (1990)]. By diagonalizing the vibrational Hamiltonian in the Fermi-system basis, the vibrational characters of all vibrational levels can be determined unambiguously. It is shown that the bending mode cannot be treated separately from the coupled stretching modes, particularly at vibrational energies of more than 2000 cm-1. Based on our force field, the structure of the Coriolis interactions in the C ˜ state of SO2 is also discussed. We identify the origin of the alternating patterns in the effective C rotational constants of levels in the vibrational progressions of the symmetry-breaking mode, νβ (which correlates with the antisymmetric stretching mode in our assignment scheme).

  9. Terahertz spectrum and normal-mode relaxation in pentaerythritol tetranitrate: effect of changes in bond-stretching force-field terms.

    Science.gov (United States)

    Pereverzev, Andrey; Sewell, Thomas D

    2011-06-28

    Terahertz (THz) active normal-mode relaxation in crystalline pentaerythritol tetranitrate (PETN) was studied using classical molecular dynamics simulations for energy and density conditions corresponding to room temperature and atmospheric pressure. Two modifications to the fully flexible non-reactive force field due to Borodin et al. [J. Phys. Chem. B 112, 734 (2008)] used in a previous study of THz-active normal-mode relaxation in PETN [J. Chem. Phys. 134, 014513 (2011)] were considered to assess the sensitivity of the earlier predictions to details of the covalent bond-stretching terms in the force field. In the first modification the harmonic bond-stretching potential was replaced with the Morse potential to study the effect of bond anharmonicity on the THz-region mode relaxation. In the second modification the C-H and nitro-group N-O bond lengths were constrained to constant values to mimic lower quantum occupation numbers for those high-frequency modes. The results for relaxation times of the initially excited modes were found to be insensitive to either force-field modification. Overall time scales for energy transfer to other modes in the system were essentially unaffected by the force-field modifications, whereas the detailed pathways by which the energy transfer occurs are more complicated for the Morse potential than for the harmonic-bond and fixed-bond cases. Terahertz infrared absorption spectra constructed using calculated normal-mode frequencies, transition dipoles, and relaxation times for THz-active modes were compared to the spectra obtained from the Fourier transform of the dipole-dipole time autocorrelation function (DDACF). Results from the two approaches are in near agreement with each other and with experimental results in terms of main peak positions. Both theoretical methods yield narrower peaks than observed experimentally and in addition predict a weaker peak at ω ∼ 50 cm(-1) that is weak or absent experimentally. Peaks obtained using

  10. Families of Fokker-Planck equations and the associated entropic form for a distinct steady-state probability distribution with a known external force field.

    Science.gov (United States)

    Asgarani, Somayeh

    2015-02-01

    A method of finding entropic form for a given stationary probability distribution and specified potential field is discussed, using the steady-state Fokker-Planck equation. As examples, starting with the Boltzmann and Tsallis distribution and knowing the force field, we obtain the Boltzmann-Gibbs and Tsallis entropies. Also, the associated entropy for the gamma probability distribution is found, which seems to be in the form of the gamma function. Moreover, the related Fokker-Planck equations are given for the Boltzmann, Tsallis, and gamma probability distributions.

  11. Model parameters for simulation of physiological lipids

    Science.gov (United States)

    McGlinchey, Nicholas

    2016-01-01

    Coarse grain simulation of proteins in their physiological membrane environment can offer insight across timescales, but requires a comprehensive force field. Parameters are explored for multicomponent bilayers composed of unsaturated lipids DOPC and DOPE, mixed‐chain saturation POPC and POPE, and anionic lipids found in bacteria: POPG and cardiolipin. A nonbond representation obtained from multiscale force matching is adapted for these lipids and combined with an improved bonding description of cholesterol. Equilibrating the area per lipid yields robust bilayer simulations and properties for common lipid mixtures with the exception of pure DOPE, which has a known tendency to form nonlamellar phase. The models maintain consistency with an existing lipid–protein interaction model, making the force field of general utility for studying membrane proteins in physiologically representative bilayers. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26864972

  12. Parametrization of coarse grained force fields for dynamic property of ethylene glycol oligomers/water binary mixtures

    CERN Document Server

    Yamazaki, Tamio

    2011-01-01

    To evaluate shear viscosity of ehylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded interactions among CG particles. Our parameterization procedure consists of three steps: 1)determination of bonded potentials, 2)scaling for time and solvent diffusivity, and 3)optimization of Lennard-Jones parameters to reproduce experimental self-diffusion coefficient data. With the determined parameters and the scaling relations, we evaluated shear viscosities of EGO/water binary mixtures, which are in close agreement with the experimental data, without any further fitting procedure. The largest simulation in this article corresponds to a 1.2 microseconds atomistic simulation for 100,000 atoms. Our CG model with the parameterization scheme for CG particles may be useful to study the dynamic properties of a liquid which contains relatively low molecular weight polymers or oligomers...

  13. Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic–ribosome complex supervised by experiment and electronic structure methods

    Directory of Open Access Journals (Sweden)

    Jörg Grunenberg

    2016-03-01

    Full Text Available We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a the isolated and b the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants. The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.

  14. The rotation-vibration structure of the SO$_2$ $\\mathrm{\\tilde{C}}^1\\mathrm{B}_2$ state explained by a new internal coordinate force field

    CERN Document Server

    Jiang, Jun; Field, R W

    2016-01-01

    A new quartic force field for the SO$_2$ $\\tilde{\\text{C}}$$^1$B$_2$ state has been derived, based on high resolution data from S$^{16}$O$_2$ and S$^{18}$O$_2$. Included are eight $b_2$ symmetry vibrational levels of S$^{16}$O$_2$ reported in the first paper of this series [G. B. Park, $\\textit{et al.}$, J. Chem. Phys. $\\textbf{144}$, 144311 (2016)]. Many of the experimental observables not included in the fit, such as the Franck-Condon intensities and the Coriolis-perturbed effective $C$ rotational constants of highly anharmonic $\\tilde{\\text{C}}$ state vibrational levels, are well reproduced using our force field. Because the two stretching modes of the $\\tilde{\\text{C}}$ state are strongly coupled via Fermi-133 interaction, the vibrational structure of the $\\tilde{\\text{C}}$ state is analyzed in a Fermi-system basis set, constructed explicitly in this work via $\\textit{partial}$ $\\textit{diagonalization}$ of the vibrational Hamiltonian. The physical significance of the Fermi-system basis is discussed in te...

  15. Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

    Institute of Scientific and Technical Information of China (English)

    ZHANG; John; ZengHui

    2010-01-01

    Molecular dynamics simulations based on AMBER force fields(ff96 and ff03) and generalized Born models(igb1 and igb5) have been carried out in order to study folding/unfolding of the Trp-cage mini-protein TC5b.The thermodynamic properties of TC5b were found to be sensitive to the specific version of the solvation model and force field employed.When the ff96/igb5 combination was used,the predicted melting temperature from unfolding simulations was in good agreement with the experimental value of 315 K,but the folding simulation did not converge.The most stable thermodynamic profile in both folding and unfolding simulations was obtained when the ff03/igb5 combination was employed,and the predicted melting temperature was about 345 K,showing over-stabilization of the protein.Simulations using the igb1 version in combination with ff96 or ff03 were difficult to converge within the simulation time limit(50 ns).

  16. Conformational and Dynamic Properties of Poly(ethylene oxide) in an Ionic Liquid: Development and Implementation of a First-Principles Force Field.

    Science.gov (United States)

    McDaniel, Jesse G; Choi, Eunsong; Son, Chang-Yun; Schmidt, J R; Yethiraj, Arun

    2016-01-14

    The conformational properties of polymers in ionic liquids are of fundamental interest but not well understood. Atomistic and coarse-grained molecular models predict qualitatively different results for the scaling of chain size with molecular weight, and experiments on dilute solutions are not available. In this work, we develop a first-principles force field for poly(ethylene oxide) (PEO) in the ionic liquid 1-butyl 3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) using symmetry adapted perturbation theory (SAPT). At temperatures above 400 K, simulations employing both the SAPT and OPLS-AA force fields predict that PEO displays ideal chain behavior, in contrast to previous simulations at lower temperature. We therefore argue that the system shows a transition from extended to more compact configurations as the temperature is increased from room temperature to the experimental lower critical solution temperature. Although polarization is shown to be important, its implicit inclusion in the OPLS-AA force is sufficient to describe the structure and energetics of the mixture. The simulations emphasize the difference between ionic liquids from typical solvents for polymers.

  17. Atomistic simulations of a solid/liquid interface: a combined force field and first principles approach to the structure and dynamics of acetonitrile near an anatase surface

    Energy Technology Data Exchange (ETDEWEB)

    Schiffmann, Florian; Hutter, Juerg; VandeVondele, Joost [Physical Chemistry Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich (Switzerland)

    2008-02-13

    The acetonitrile/anatase(101) interface can be considered a prototypical interface between an oxide and a polar aprotic liquid, and is common in dye sensitized solar cells. Using first principles molecular dynamics simulations of a slab of TiO{sub 2} in contact with neat acetonitrile (MeCN), the liquid structure near this interface has been characterized. Furthermore, in order to investigate properties that require extensive sampling, a classical force field to describe the MeCN/TiO{sub 2} interaction has been optimized, and we show that this force field accurately describes the structure near the interface. We find a surprisingly strong interaction of MeCN with TiO{sub 2}, which leads to an ordered first MeCN layer displaying a significantly enhanced molecular dipole. The strong dipolar interactions between solvent molecules lead to pronounced layering further away from the interface, each successive layer having an alternate orientation of the molecular dipoles. At least seven distinct solvent layers (approximately 12 A) can be discerned in the orientational distribution function. The observed structure also strongly suppresses diffusion parallel to the interface in the first nanometer of the liquid. These results show that the properties of the liquid near the interface differ from those in the bulk, which suggests that solvation near the interface will be distinctly different from solvation in the bulk.

  18. 3D physical modeling of anisotropic grain growth at high temperature in local strong magnetic force field

    Directory of Open Access Journals (Sweden)

    Eric Beaugnon

    2008-01-01

    Full Text Available A new mechanism based on the effect of local magnetic forces on diffusing ions around a growing ferromagnetic precipitate is proposed. A 3D simulation based only on physical parameters is undertaken in which main assumption is of interface limited growth controlled by the effect of both curvature and local magnetic field distortion. Although usually neglected in magnetic field effect mechanisms, it is shown that these local magnetic forces acting on a single paramagnetic ion can change markedly affect the growth process and induce strong shape anisotropy.

  19. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field.

    Science.gov (United States)

    Lamoureux, Guillaume; Roux, Benoît

    2006-02-23

    A polarizable potential function for the hydration of alkali and halide ions is developed on the basis of the recent SWM4-DP water model [Lamoureux, G.; MacKerell, A. D., Jr.; Roux, B. J. Chem. Phys. 2003, 119, 5185]. Induced polarization is incorporated using classical Drude oscillators that are treated as auxiliary dynamical degrees of freedom. The ions are represented as polarizable Lennard-Jones centers, whose parameters are optimized to reproduce the binding energies of gas-phase monohydrates and the hydration free energies in the bulk liquid. Systematic exploration of the parameters shows that the monohydrate binding energies can be consistent with a unique hydration free energy scale if the computed hydration free energies incorporate the contribution from the air/water interfacial electrostatic potential (-540 mV for SWM4-DP). The final model, which can satisfyingly reproduce both gas and bulk-phase properties, corresponds to an absolute scale in which the intrinsic hydration free energy of the proton is -247 kcal/mol.

  20. Development of a Modified Embedded Atom Force Field for Zirconium Nitride Using Multi-Objective Evolutionary Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Narayanan, Badri; Sasikumar, Kiran; Mei, Zhi-Gang; Kinaci, Alper; Sen, Fatih G.; Davis, Michael J.; Gray, Stephen K.; Chan, Maria K. Y.; Sankaranarayanan, Subramanian K. R. S.

    2016-07-07

    Zirconium nitride (ZrN) exhibits exceptional mechanical, chemical, and electrical properties, which make it attractive for a wide range of technological applications, including wear-resistant coatings, protection from corrosion, cutting/shaping tools, and nuclear breeder reactors. Despite its broad usability, an atomic scale understanding of the superior performance of ZrN, and its response to external stimuli, for example, temperature, applied strain, and so on, is not well understood. This is mainly due to the lack of interatomic potential models that accurately describe the interactions between Zr and N atoms. To address this challenge, we develop a modified embedded atom method (MEAM) interatomic potential for the Zr–N binary system by training against formation enthalpies, lattice parameters, elastic properties, and surface energies of ZrN (and, in some cases, also Zr3N4) obtained from density functional theory (DFT) calculations. The best set of MEAM parameters are determined by employing a multiobjective global optimization scheme driven by genetic algorithms. Our newly developed MEAM potential accurately reproduces structure, thermodynamics, energetic ordering of polymorphs, as well as elastic and surface properties of Zr–N compounds, in excellent agreement with DFT calculations and experiments. As a representative application, we employed molecular dynamics simulations based on this MEAM potential to investigate the atomic scale mechanisms underlying fracture of bulk and nanopillar ZrN under applied uniaxial strains, as well as the impact of strain rate on their mechanical behavior. These simulations indicate that bulk ZrN undergoes brittle fracture irrespective of the strain rate, while ZrN nanopillars show quasi-plasticity owing to amorphization at the crack front. The MEAM potential for Zr–N developed in this work is an invaluable tool to investigate atomic-scale mechanisms underlying the response of ZrN to external stimuli (e.g, temperature

  1. Development and validation of a ReaxFF reactive force field for Fe/Al/Ni alloys: molecular dynamics study of elastic constants, diffusion, and segregation.

    Science.gov (United States)

    Shin, Yun Kyung; Kwak, Hyunwook; Zou, Chenyu; Vasenkov, Alex V; van Duin, Adri C T

    2012-12-13

    We have developed a ReaxFF force field for Fe/Al/Ni binary alloys based on quantum mechanical (QM) calculations. In addition to the various bulk phases of the binary alloys, the (100), (110) and (111) surface energies and adatom binding energies were included in the training set for the force field parametrization of the Fe/Al/Ni binary alloys. To validate these optimized force fields, we studied (i) elastic constants of the binary alloys at finite temperatures, (ii) diffusivity of alloy components in Al/Ni alloy, and (iii) segregation on the binary alloy surfaces. First, we calculated linear elastic constants of FeAl, FeNi(3), and Ni(3)Al in the temperature range 300 to 1100 K. The temperature dependences of the elastic constants of these three alloys, showing a decrease in C(11), C(12), and C(44) as temperature increases, were in good agreement with the experimental results. We also performed ReaxFF molecular dynamics (MD) simulations for Al or Ni diffusion in the system modeled as Al/Ni mixed layers with the linear composition gradients. At 1000 K, Al diffusivity at the pure Al end was 2 orders of magnitude larger than that in the Al trace layers, probably explaining the nature of different diffusion behavior between molten metals and alloys. However, the diffusivity of Ni at the pure Ni end was only slightly larger than that in the Ni trace layers at the system temperature much lower than the melting temperature of Ni. Third, we investigated the surface segregation in L1(2)-Fe(3)Al, Fe(3)Ni, and Ni(3)Al clusters at high temperature (2500 K). From the analysis of composition distribution of the alloy components from the bulk to the surface layer, it was found that the degree of segregation depended on the chemical composition of the alloy. Al surface segregation occurred most strongly in Fe(3)Al, whereas it occurred most weakly in Ni(3)Al. These results may support the segregation mechanism that surface segregation results from the interplay between the

  2. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

    Science.gov (United States)

    Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

    2014-09-04

    We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar

  3. First-Principles United Atom Force Field for the Ionic Liquid BMIM(+)BF4(-): An Alternative to Charge Scaling.

    Science.gov (United States)

    Son, Chang Yun; McDaniel, Jesse G; Schmidt, J R; Cui, Qiang; Yethiraj, Arun

    2016-04-14

    Molecular dynamics study of ionic liquids (ILs) is a challenging task. While accurate fully polarizable atomistic models exist, they are computationally too demanding for routine use. Most nonpolarizable atomistic models predict diffusion constants that are much lower than experiment. Scaled charge atomistic models are cost-effective and give good results for single component ILs but are in qualitative error for the phase behavior of mixtures, due to inaccurate prediction of the IL cohesive energy. In this work, we present an alternative approach for developing computationally efficient models that importantly preserves both the correct dynamics and cohesive energy of the IL. Employing a "top-down" approach, a hierarchy of coarse-grained models for BMIM(+)BF4(-) are developed by systematically varying the polarization/atomic resolution of the distinct functional groups. Parametrization is based on symmetry-adapted perturbation theory (SAPT) calculations involving the homomolecular species; all cross interactions are obtained from mixing rules, and there are no adjustable parameters. We find that enhanced dynamics from a united-atom description counteracts the effect of reduced polarization, enabling computationally efficient models that exhibit quantitative agreement with experiment for both static and dynamic properties. We give explicit suggestions for reduced-description models that are computationally more efficient, more accurate, and more fundamentally sound than existing nonpolarizable atomistic models.

  4. Vibrational Frequencies and Spectroscopic Constants for 1(sup 3)A' HNC and 1(sup 3)A' HOC+ from High-Accuracy Quartic Force Fields

    Science.gov (United States)

    Fortenberry, Ryan C.; Crawford, T. Daniel; Lee, Timothy J.

    2014-01-01

    The spectroscopic constants and vibrational frequencies for the 1(sup 3)A' states of HNC, DNC, HOC+, and DOC+ are computed and discussed in this work. The reliable CcCR quartic force field based on high-level coupled cluster ab initio quantum chemical computations is exclusively utilized to provide the anharmonic potential. Then, second order vibrational perturbation theory and vibrational configuration interaction methods are employed to treat the nuclear Schroedinger equation. Second-order perturbation theory is also employed to provide spectroscopic data for all molecules examined. The relationship between these molecules and the corresponding 1(sup 3)A' HCN and HCO+ isomers is further developed here. These data are applicable to laboratory studies involving formation of HNC and HOC+ as well as astronomical observations of chemically active astrophysical environments.

  5. Density functional theory study, FT-IR and FT-Raman spectra and SQM force field calculation for vibrational analysis of 1, 3-Bis (hydroxymethyl) benzimidazolin-2-one.

    Science.gov (United States)

    Joseph, Lynnette; Sajan, D; Chaitanya, K; Devarajegowda, H C; Isac, Jayakumary

    2013-10-01

    FT-IR and FT-Raman spectra of 1, 3-Bis (hydroxymethyl) benzimidazolin-2-one were recorded and analyzed in the solid phase. The optimized molecular geometry and vibrational wavenumbers have also been calculated in optimized structure by using DFT method. Scaled quantum mechanical force fields have also been used to calculate potential energy distributions in order to make conspicuous vibrational assignments. The red shifting of the O-H stretching wavenumber is due to the formation of O-H···O intermolecular hydrogen bonding. The lowering and splitting of the carbonyl stretching vibrational modes is assigned to the intermolecular association based on C=O···H type hydrogen bonding in the molecule. Chemical interpretation of hyperconjugative interactions was done by natural bond orbital analysis.

  6. Benchmark Database on Isolated Small Peptides Containing an Aromatic Side Chain: Comparison Between Wave Function and Density Functional Theory Methods and Empirical Force Field

    Energy Technology Data Exchange (ETDEWEB)

    Valdes, Haydee; Pluhackova, Kristyna; Pitonak, Michal; Rezac, Jan; Hobza, Pavel

    2008-03-13

    A detailed quantum chemical study on five peptides (WG, WGG, FGG, GGF and GFA) containing the residues phenylalanyl (F), glycyl (G), tryptophyl (W) and alanyl (A)—where F and W are of aromatic character—is presented. When investigating isolated small peptides, the dispersion interaction is the dominant attractive force in the peptide backbone–aromatic side chain intramolecular interaction. Consequently, an accurate theoretical study of these systems requires the use of a methodology covering properly the London dispersion forces. For this reason we have assessed the performance of the MP2, SCS-MP2, MP3, TPSS-D, PBE-D, M06-2X, BH&H, TPSS, B3LYP, tight-binding DFT-D methods and ff99 empirical force field compared to CCSD(T)/complete basis set (CBS) limit benchmark data. All the DFT techniques with a ‘-D’ symbol have been augmented by empirical dispersion energy while the M06-2X functional was parameterized to cover the London dispersion energy. For the systems here studied we have concluded that the use of the ff99 force field is not recommended mainly due to problems concerning the assignment of reliable atomic charges. Tight-binding DFT-D is efficient as a screening tool providing reliable geometries. Among the DFT functionals, the M06-2X and TPSS-D show the best performance what is explained by the fact that both procedures cover the dispersion energy. The B3LYP and TPSS functionals—not covering this energy—fail systematically. Both, electronic energies and geometries obtained by means of the wave-function theory methods compare satisfactorily with the CCSD(T)/CBS benchmark data.

  7. 电磁力场作用下凝固界面前沿颗粒迁移特性的理论模型%Theoretical Model for Particle Behavior at Solidifying Front in Electromagnetic Force Field

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The particle migrating behavior at solidifying front is discussed in theory with the application of electromagnetic force field (EMFF), on the basis of foregone analysis of force upon particle ahead of solidifying front without electromagnetic force field. The critical solidification velocities of particle pushing/engulfment transition ahead of horizontal and vertical interface are derived respectively when a certain EMFF is applied. And the critical electromagnetic forces of particle pushing/engulfment transition ahead of horizontal and vertical interface are also derived separately when a certain solidifying velocity is given.

  8. Parameters for Martini sterols and hopanoids based on a virtual-site description

    NARCIS (Netherlands)

    Melo, M. N.; Ingolfsson, H. I.; Marrink, S. J.

    2015-01-01

    Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the u

  9. The chemical hardness of molecules and the band gap of solids within charge equilibration formalisms. Toward force field-based simulations of redox reactions

    Science.gov (United States)

    Müser, M. H.

    2012-04-01

    This work finds that different charge equilibration methods lead to qualitatively different responses of molecules and solids to an excess charge. The investigated approaches are the regular charge equilibration (QE), the atom-atom-charge transfer (AACT), and the split-charge equilibration (SQE) method. In QE, the hardness of molecules and the band gap of solids approaches zero at large particle numbers, affirming the claim that QE induces metallic behavior. AACT suffers from producing negative values of the hardness; moreover valence and conduction bands of solids cross. In contrast to these methods, SQE can reproduce the generic behavior of dielectric molecules or solids. Moreover, first quantitative results for the NaCl molecule are promising. The results derived in this work may have beneficial implications for the modeling of redox reactions. They reveal that by introducing formal oxidation states into force field-based simulations it will become possible to simulate redox reactions including non-equilibrium contact electrification, voltage-driven charging of galvanic cells, and the formation of zwitterionic molecules.

  10. New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2.

    Science.gov (United States)

    Ferrara, Ph; Curioni, A; Vangrevelinghe, E; Meyer, T; Mordasini, T; Andreoni, W; Acklin, P; Jacoby, E

    2006-01-01

    A recently introduced new methodology based on ultrashort (50-100 ps) molecular dynamics simulations with a quantum-refined force-field (QRFF-MD) is here evaluated in its ability both to predict protein-ligand binding affinities and to discriminate active compounds from inactive ones. Physically based scoring functions are derived from this approach, and their performance is compared to that of several standard knowledge-based scoring functions. About 40 inhibitors of cyclin-dependent kinase 2 (CDK2) representing a broad chemical diversity were considered. The QRFF-MD method achieves a correlation coefficient, R(2), of 0.55, which is significantly better than that obtained by a number of traditional approaches in virtual screening but only slightly better than that obtained by consensus scoring (R(2) = 0.50). Compounds from the Available Chemical Directory, along with the known active compounds, were docked into the ATP binding site of CDK2 using the program Glide, and the 650 ligands from the top scored poses were considered for a QRFF-MD analysis. Combined with structural information extracted from the simulations, the QRFF-MD methodology results in similar enrichment of known actives compared to consensus scoring. Moreover, a new scoring function is introduced that combines a QRFF-MD based scoring function with consensus scoring, which results in substantial improvement on the enrichment profile.

  11. High-Temperature and High-Pressure Pyrolysis of Hexadecane: Molecular Dynamic Simulation Based on Reactive Force Field (ReaxFF).

    Science.gov (United States)

    Chen, Zhuojun; Sun, Weizhen; Zhao, Ling

    2017-03-07

    As important products of heavy oil pyrolysis, heavier components such as gasoline and diesel supply the vast majority of energy demand through combustion, and lighter components such as ethylene and propylene are the main sources of industrial chemicals and plastic products. In this work, pyrolysis of hexadecane, as the model compound, was studied by reactive force field (ReaxFF) molecular simulation at high temperatures and high pressures. It was confirmed by unimolecular simulations that there exist eight different initial mechanisms all starting with C-C bond dissociation. The biradical mechanism was verified, through which the pyrolysis process can be accomplished within a shorter time. The enthalpy of reaction was calculated by the QM method, which was well consistent with ReaxFF calculation results. Multimolecular simulations showed that there is a strong dependency relationship between products distribution and temperature, as well as that between reaction rates and temperature. The optimal condition for ethylene formation in our work is 11.6 MPa and 2000 K, whereas it is best for hydrogen formation at conditions of 11.6 MPa and 3500 K. Kinetic analysis was performed with the activation energy of 113.03 kJ/mol and pre-exponential factor of 4.55 × 10(12), and it is in good agreement with previous work.

  12. Anharmonic rovibrational calculations of singlet cyclic C{sub 4} using a new ab initio potential and a quartic force field

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xiaohong; Bowman, Joel M., E-mail: jmbowma@emory.edu [Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States); Huang, Xinchuan [SETI Institute, 189 Bernardo Ave, Suite 100, Mountain View, California 94043 (United States); Lee, Timothy J., E-mail: Timothy.J.Lee@nasa.gov [MS 245-1, NASA Ames Research Center, Mofffett Field, California 94035 (United States)

    2013-12-14

    We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C{sub 4}. Vibrational fundamentals, combinations, and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configuration-interaction (VCI) approach. Agreement is within 10 cm{sup −1} between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2-QFF and MM-QFF results is also good for the C{sub 4} combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of {sup 12}C{sub 4} and two C{sub 2v}-symmetry, single {sup 13}C-substituted isotopologues are presented, which may help identification of cyclic C{sub 4} in future experimental analyses or astronomical observations.

  13. A Numerical Study of Low-Thrust Limited Power Trajectories between Coplanar Circular Orbits in an Inverse-Square Force Field

    Directory of Open Access Journals (Sweden)

    Sandro da Silva Fernandes

    2012-01-01

    Full Text Available A numerical study of optimal low-thrust limited power trajectories for simple transfer (no rendezvous between circular coplanar orbits in an inverse-square force field is performed by two different classes of algorithms in optimization of trajectories. This study is carried out by means of a direct method based on gradient techniques and by an indirect method based on the second variation theory. The direct approach of the trajectory optimization problem combines the main positive characteristics of two well-known direct methods in optimization of trajectories: the steepest-descent (first-order gradient method and a direct second variation (second-order gradient method. On the other hand, the indirect approach of the trajectory optimization problem involves two different algorithms of the well-known neighboring extremals method. Several radius ratios and transfer durations are considered, and the fuel consumption is taken as the performance criterion. For small-amplitude transfers, the results are compared to the ones provided by a linear analytical theory.

  14. Theoretical Studies of AQP4 in Water and Gas Phases, Nano Simulation of the Monte Carlo Method by Molecular Mechanics Force Fields

    Directory of Open Access Journals (Sweden)

    Ebrahim Shahmansoorian

    2014-09-01

    Full Text Available Aquaporins are membrane water channels that play critical roles in controlling the water contents of cells. These channels are widely distributed in all kingdoms of life, including bacteria, plants, and mammals. More than ten different aquaporins have been found in human body, and several diseases, such as congenital cataracts and nephrogenic diabetes insipidus, are connected to the impaired function of these channels. They form tetramers in the cell membrane, and facilitate the transport of water and, in some cases, other small solutes across the membrane. However, the water pores are completely impermeable to charged species, such as protons, a remarkable property that is critical for the conservation of membrane's electrochemical potential, but paradoxical at the same time, since protons can usually be transferred readily through water molecules. The present investigation is profound manifesting of thermodynamics characteristics of the impressive AQP4 role in biology. To clarify the majestic AQP4 role in biology, it was modeled. So we use pc-based modeling and simulation software package called HyperChem by applying four different force fields. The results of our simulations have now provided new insight into the optimal stability of AQP4.

  15. Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field.

    Science.gov (United States)

    Zhou, Chen-Yang; Jiang, Fan; Wu, Yun-Dong

    2015-11-10

    To test whether our recently developed residue-specific force field RSFF2 can reproduce the mutational effect on the thermal stability of Trp-cage mini-protein and decipher its detailed folding mechanism, we carried out long-time replica-exchange molecular dynamics (REMD) simulations on five Trp-cage variants, including TC5b and TC10b. Initiated from their unfolded structures, the simulations not only well-reproduce their experimental structures but also their melting temperatures and folding enthalpies reasonably well. For each Trp-cage variant, the overall folding free energy landscape is apparently two-state, but some intermediate states can be observed when projected on more detailed coordinates. We also found different variants have the same major folding pathway, including the well formed PII-helix in the unfolded state, the formation of W6-P12/P18/P19 contacts and the α-helix before the transition state, the following formation of most native contacts, and the final native loop formation. The folding mechanism derived here is consistent with many previous simulations and experiments.

  16. Frequency and zero-point vibrational energy scale factors for double-hybrid density functionals (and other selected methods): can anharmonic force fields be avoided?

    Science.gov (United States)

    Kesharwani, Manoj K; Brauer, Brina; Martin, Jan M L

    2015-03-05

    We have obtained uniform frequency scaling factors λ(harm) (for harmonic frequencies), λ(fund) (for fundamentals), and λ(ZPVE) (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.

  17. Automatic generation of force fields and property surfaces for use in variational vibrational calculations of anharmonic vibrational energies and zero-point vibrational averaged properties.

    Science.gov (United States)

    Kongsted, Jacob; Christiansen, Ove

    2006-09-28

    An automatic and general procedure for the calculation of geometrical derivatives of the energy and general property surfaces for molecular systems is developed and implemented. General expressions for an n-mode representation are derived, where the n-mode representation includes only the couplings between n or less degrees of freedom. The general expressions are specialized to derivative force fields and property surfaces, and a scheme for calculation of the numerical derivatives is implemented. The implementation is interfaced to electronic structure programs and may be used for both ground and excited electronic states. The implementation is done in the context of a vibrational structure program and can be used in combination with vibrational self-consistent field (VSCF), vibrational configuration interaction (VCI), vibrational Moller-Plesset, and vibrational coupled cluster calculations of anharmonic wave functions and calculation of vibrational averaged properties at the VSCF and VCI levels. Sample calculations are presented for fundamental vibrational energies and vibrationally averaged dipole moments and frequency dependent polarizabilities and hyperpolarizabilities of water and formaldehyde.

  18. Structural criteria for the rational design of selective ligands. Extension of the MM3 force field to aliphatic ether complexes of the alkali and alkaline earth cations

    Energy Technology Data Exchange (ETDEWEB)

    Hay, B.P.; Rustad, J.R. (Pacific Northwest Lab., Richland, WA (United States))

    1994-07-13

    Structural requirements for strain-free metal ion complexation by an aliphatic ether group are investigated through the use of both ab initio molecular orbital and molecular mechanics calculations. Hartree-Fock calculations on simple models, M-O(Me)[sub 2] and M-O(Me)(Et), reveal a preference for trigonal planar geometry when aliphatic ether oxygens are coordinated to alkali and alkaline earth cations. This preference is found to be strongest in small, high-valent cations and weakest in large, low-valent cations. Results from the Hartree-Fock calculations are used to extend the MM3 force field for calculation on aliphatic ether complexes with the alkali (Li to Cs) and alkaline earth (Mg to Ba) cations. The resulting molecular model (i) reproduces the experimental crystal structures of 51 different complexes of multidentate ethers with alkali and alkaline earth cations, (ii) explains experimental trends in the structure of five-membered chelate rings of aliphatic ethers, (iii) reveals a fundamental difference between the metal ion size selectivity of five-membered chelate rings of ethers versus that of amines, and (iv) rationalizes trends in the stability of four potassium complexes with the diasteriomers of dicyclohexyl-18-crown-6. 40 refs., 9 figs., 5 tabs.

  19. Force field based molecular dynamics simulations in highly conducting compounds of poly(aniline). A comparison with quasi-elastic neutron scattering measurements

    Energy Technology Data Exchange (ETDEWEB)

    Sniechowski, M. [Laboratoire de Spectrometrie Physique, UMR5588 (CNRS-UJF), Universite J. Fourier, Grenoble I, Domaine Universitaire, B.P. 87, 38402 St. Martin d' Heres, Cedex (France); Faculty of Physics and Nuclear Techniques, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland); Djurado, D. [Laboratoire de Physique des Metaux Synthetiques, CEA Grenoble, DRFMC/SI3M/SPrAM, UMR 5819 (CEA/CNRS/UJF), 17 Rue des Martyrs, 38054 Grenoble, Cedex 9 (France)], E-mail: djurado@drfmc.ceng.cea.fr; Bee, M. [Laboratoire de Spectrometrie Physique, UMR5588 (CNRS-UJF), Universite J. Fourier, Grenoble I, Domaine Universitaire, B.P. 87, 38402 St. Martin d' Heres, Cedex (France); Institut Laue Langevin, 6 rue Jules Horovitz, B.P. 156, 38042 Grenoble, Cedex 9 (France); Gonzalez, M.A. [Institut Laue Langevin, 6 rue Jules Horovitz, B.P. 156, 38042 Grenoble, Cedex 9 (France); Johnson, M.R. [Institut Laue Langevin, 6 rue Jules Horovitz, B.P. 156, 38042 Grenoble, Cedex 9 (France); Rannou, P. [Laboratoire de Physique des Metaux Synthetiques, CEA Grenoble, DRFMC/SI3M/SPrAM, UMR 5819 (CEA/CNRS/UJF), 17 Rue des Martyrs, 38054 Grenoble, Cedex 9 (France); Dufour, B. [Laboratoire de Physique des Metaux Synthetiques, CEA Grenoble, DRFMC/SI3M/SPrAM, UMR 5819 (CEA/CNRS/UJF), 17 Rue des Martyrs, 38054 Grenoble, Cedex 9 (France); Luzny, W. [Faculty of Physics and Nuclear Techniques, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Cracow (Poland)

    2005-10-31

    Dynamics of counter-ions in poly(aniline) doped with di-(2-butoxyethoxyethyl)ester of 4-sulfophthalic acid have been simulated using force field based molecular dynamics involving a semi-empirical charge equilibration procedure and charge rescaling based on DFT calculations. Due to particular relaxational and structural characteristics of such 'plastdoped' poly(anilines), these simulations have proved to be a very effective tool for reproducing the main structural and dynamic features of the material. The experiment/simulation comparison for dynamics is very good in the 10{sup -10}-10{sup -13} s time range. In particular, mean square displacements extracted from the molecular dynamics simulations for atoms in the counter-ions are in good agreement with the analytical model used to analyse the quasi-elastic neutron scattering data. The use of a larger simulation box and longer simulation time give good agreement in the extended time domain and reveal a dynamical heterogeneity between the counter-ions that was not foreseen in the analytical model.

  20. Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.

    Science.gov (United States)

    Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

    2017-03-05

    We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

  1. Comparison of force fields on the basis of various model approaches--how to design the best model for the [CnMIM][NTf2] family of ionic liquids.

    Science.gov (United States)

    Köddermann, Thorsten; Reith, Dirk; Ludwig, Ralf

    2013-10-07

    In this contribution, we present two new united-atom force fields (UA-FFs) for 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [C(n)MIM][NTf(2)] (n=1, 2, 4, 6, 8) ionic liquids (ILs). One is parametrized manually, and the other is developed with the gradient-based optimization workflow (GROW). By doing so, we wanted to perform a hard test to determine how researchers could benefit from semiautomated optimization procedures. As with our already published all-atom force field (AA-FF) for [C(n)MIM][NTf(2)] (T. Köddermann, D. Paschek, R. Ludwig, ChemPhysChem- 2007, 8, 2464), the new force fields were derived to fit experimental densities, self-diffusion coefficients, and NMR rotational correlation times for the IL cation and for water molecules dissolved in [C(2)MIM][NTf(2)]. In the manual force field, the alkyl chains of the cation and the CF3 groups of the anion were treated as united atoms. In the GROW force field, only the alkyl chains of the cation were united. All other parts of the structures of the ions remained unchanged to prevent any loss of physical information. Structural, dynamic, and thermodynamic properties such as viscosity, cation rotational correlation times, and heats of vaporization calculated with the new force fields were compared with values simulated with the previous AA-FF and the experimental data. All simulated properties were in excellent agreement with the experimental values. Altogether, the UA-FFs are slightly superior for speed-up reasons. The UA-FF speeds up the simulation by about 100 % and reduces the demanded disk space by about 78 %. More importantly, real time and efforts to generate force fields could be significantly reduced by utilizing GROW. The real time for the GROW parametrization in this work was 2 months. Manual parametrization, in contrast, may take up to 12 months, and this is, therefore, a significant increase in speed, though it is difficult to estimate the duration of manual parametrization.

  2. Systematic parameter inference in stochastic mesoscopic modeling

    Science.gov (United States)

    Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

    2017-02-01

    We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

  3. The Nature of Noncovalent Interactions in Catenane Supramolecular Complexes: Calibrating the MM3 Force Field with ab initio, DFT and SAPT Methods

    Science.gov (United States)

    Simeon, Tomekia M.; Ratner, Mark A.; Schatz, George C.

    2013-01-01

    The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H⋯O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3] catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H⋯O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H⋯O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, and we find that electrostatic interactions dominate the [C-H⋯O] hydrogen-bonding interactions while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interactions energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correct have important differences compared to DFT-SAPT while HF and even MP2 results are in poor agreement with DFT-SAPT. PMID:23941280

  4. Nature of noncovalent interactions in catenane supramolecular complexes: calibrating the MM3 force field with ab initio, DFT, and SAPT methods.

    Science.gov (United States)

    Simeon, Tomekia M; Ratner, Mark A; Schatz, George C

    2013-08-22

    The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.

  5. Topology-based automatical assignment of force field atom types%基于拓扑子集的势场原子类型的派定

    Institute of Scientific and Technical Information of China (English)

    陈健; 冯长根

    2002-01-01

    对于除了标准氨基酸、核酸残基以外的一般分子,派定分子中原子的原子类型,确定原子类型在不同分子势场之间的转换,这些工作一般是由人工来完成.本文从分子拓扑学的角度解析了分子势场的原子类型(atom type)定义,以基于分子拓扑子集取代原子类型定义的分子片断为途径,实现势场原子类型的计算机自动派定.该方法易于编程,并能满足用户调整原子类型的意愿.%For general molecules the atom types are usually manually assigned rather than automatically. And the conventional definitionof the atom types for force fields represents structural fragments in the structure of a molecule. From the topological point of view, eachof such fragments is one-to-one mapped on a topological subset of molecules of interest, which can be used as the topological definitionof atom types in place of their conventional semantic definition of atom types. Based upon the topological definition, the authors in thispresent paper put forward an approach to the automatical assignment of atom types, which proves to be a favorite for the actual researchpractice.

  6. Effects of temperature on the thermodynamic and dynamical properties of glycerol-water mixtures: a computer simulation study of three different force fields.

    Science.gov (United States)

    Akinkunmi, Frederick O; Jahn, David A; Giovambattista, Nicolas

    2015-05-21

    Glycerol-water solutions are relevant in technological and scientific applications, such as in the preservation of biomolecules and tissues at low temperatures. We perform molecular dynamics simulations of glycerol-water mixtures with glycerol molar fractions of χg = 0-100% at P = 0.1 MPa and T = 210-460 K. We focus on the effects of temperature and concentration on the thermodynamic (density ρ, thermal expansion coefficient αP, isobaric specific heat cP, compressibility κT) and dynamical (glycerol and water diffusion coefficients, Dg and Dw) properties of the mixtures. In particular, we test the sensitivity of computer simulation results to the glycerol force field and water model (TIP3P and TIP4P/2005) employed. All mixture models underestimate ρ at high T and tend to overestimate ρ at low T; only the mixture model based on TIP4P/2005 water exhibits a density maximum at low χg, as expected. All models overestimate αP, cP, and κT; they are able to reproduce qualitatively the T dependence of αP and κT but fail in the case of cP. In all cases, Dg and Dw follow the Vogel-Tamman-Fulcher equation and decouple at low T, with Dw/Dg increasing upon cooling. Overall, the mixture based on TIP4P/2005 water provides better thermodynamic and dynamical properties than the mixtures based on TIP3P water, even at χg = 20%.

  7. ReaxFF-lg: correction of the ReaxFF reactive force field for London dispersion, with applications to the equations of state for energetic materials.

    Science.gov (United States)

    Liu, Lianchi; Liu, Yi; Zybin, Sergey V; Sun, Huai; Goddard, William A

    2011-10-13

    The practical levels of density functional theory (DFT) for solids (LDA, PBE, PW91, B3LYP) are well-known not to account adequately for the London dispersion (van der Waals attraction) so important in molecular solids, leading to equilibrium volumes for molecular crystals ~10-15% too high. The ReaxFF reactive force field is based on fitting such DFT calculations and suffers from the same problem. In the paper we extend ReaxFF by adding a London dispersion term with a form such that it has low gradients (lg) at valence distances leaving the already optimized valence interactions intact but behaves as 1/R(6) for large distances. We derive here these lg corrections to ReaxFF based on the experimental crystal structure data for graphite, polyethylene (PE), carbon dioxide, and nitrogen and for energetic materials: hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX), pentaerythritol tetranitrate (PETN), 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), and nitromethane (NM). After this dispersion correction the average error of predicted equilibrium volumes decreases from 18.5 to 4.2% for the above systems. We find that the calculated crystal structures and equation of state with ReaxFF-lg are in good agreement with experimental results. In particular, we examined the phase transition between α-RDX and γ-RDX, finding that ReaxFF-lg leads to excellent agreement for both the pressure and volume of this transition occurring at ~4.8 GPa and ~2.18 g/cm(3) density from ReaxFF-lg vs 3.9 GPa and ~2.21 g/cm(3) from experiment. We expect ReaxFF-lg to improve the descriptions of the phase diagrams for other energetic materials.

  8. MCPB.py: A Python Based Metal Center Parameter Builder.

    Science.gov (United States)

    Li, Pengfei; Merz, Kenneth M

    2016-04-25

    MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

  9. Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.

    Science.gov (United States)

    Kukol, Andreas

    2009-03-10

    United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.

  10. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.

    Science.gov (United States)

    Morgado, Claudio A; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jirí

    2010-04-14

    We have performed reference quantum-chemical calculations for about 130 structures of adenine dimers in stacked conformations, with special attention given to dimers that are either vertically compressed (parallel structures) or contain close interatomic contacts (non-parallel structures). Such geometries are sampled during thermal fluctuations of nucleic acids and contribute to the local conformational variability of these systems. Their theoretical characterization requires a good description of interaction energies in the short-range repulsion region. The reference calculations have been performed with the CBS(T) method, i.e., MP2/CBS computations corrected for higher-order electron-correlation effects using the CCSD(T) method. These benchmark data have been used to examine the performance of the DFT-D, SCS(MI)-MP2, MP2.5, M06-2X and CBS(SCS-D) quantum-mechanical methods, and of the AMBER Cornell et al. force field. The present results, as well as those of our previous study on stacked uracil dimers, confirm that the force field severely exaggerates the repulsion at short intermolecular distances. This behavior complicates the use of the force field in scans of the stacking-energy dependence on local conformational parameters in nucleic acids. Compared against the previous results obtained in the uracil dimer study, the performance of DFT-D to describe stacking at short intermolecular distances has worsened, showing for the adenine dimers a larger exaggeration of the repulsion, especially for structures where the monomers are parallel to each other. Despite these deviations, the performance of DFT-D is still reasonably good and this method provides, for example, a relatively inexpensive way to monitor stacking energies along molecular dynamics trajectories. The best performers are the MP2.5, SCS(MI)-MP2, and CBS(SCS-D) methods. In addition, the energy profiles given by the SCS(MI)-MP2 and CBS(SCS-D) methods are the ones that most closely resemble the CBS(T) data

  11. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields.

    Science.gov (United States)

    Xiao, Yuming; Koutmos, Markos; Case, David A; Coucouvanis, Dimitri; Wang, Hongxin; Cramer, Stephen P

    2006-05-14

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies. The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT

  12. Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.

    Science.gov (United States)

    Mozolewska, Magdalena A; Krupa, Paweł; Zaborowski, Bartłomiej; Liwo, Adam; Lee, Jooyoung; Joo, Keehyoung; Czaplewski, Cezary

    2016-11-28

    Recently, we developed a new approach to protein-structure prediction, which combines template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) force field. In this approach, restrained multiplexed replica exchange molecular dynamics simulations with UNRES, with the C(α)-distance and virtual-bond-dihedral-angle restraints derived from knowledge-based models are carried out. In this work, we report a test of this approach in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11), in which we used the template-based models from early-stage predictions by the LEE group CASP11 server (group 038, called "nns"), and further improvement of the method. The quality of the models obtained in CASP11 was better than that resulting from unrestrained UNRES simulations; however, the obtained models were generally worse than the final nns models. Calculations with the final nns models, performed after CASP11, resulted in substantial improvement, especially for multi-domain proteins. Based on these results, we modified the procedure by deriving restraints from models from multiple servers, in this study the four top-performing servers in CASP11 (nns, BAKER-ROSETTASERVER, Zhang-server, and QUARK), and implementing either all restraints or only the restraints on the fragments that appear similar in the majority of models (the consensus fragments), outlier models discarded. Tests with 29 CASP11 human-prediction targets with length less than 400 amino-acid residues demonstrated that the consensus-fragment approach gave better results, i.e., lower α-carbon root-mean-square deviation from the experimental structures, higher template modeling score, and global distance test total score values than the best of the parent server models. Apart from global improvement (repacking and improving the orientation of domains and other substructures), improvement was also reached for template-based modeling

  13. Levy diffusion in a force field, huber relaxation kinetics, and nonequilibrium thermodynamics: H theorem for enhanced diffusion with Levy white noise

    Science.gov (United States)

    Vlad; Ross; Schneider

    2000-08-01

    A characteristic functional approach is suggested for Levy diffusion in disordered systems with external force fields. We study the overdamped motion of an ensemble of independent particles and assume that the force acting upon one particle is made up of two additive components: a linear term generated by a harmonic potential and a second term generated by the interaction with the disordered system. The stochastic properties of the second term are evaluated by using Huber's approach to complex relaxation [Phys. Rev. B 31, 6070 (1985)]. We assume that the interaction between a moving particle and the environment can be expressed by the contribution of a large number of relaxation channels, each channel having a very small probability of being open and obeying Poisson statistics. Two types of processes are investigated: (a) Levy diffusion with static disorder for which the fluctuations of the random force are frozen and last forever and (b) diffusion with strong dynamic disorder and independent Levy fluctuations (Levy white noise). In both cases we show that the probability distribution of the position of a diffusing particle tends towards a stationary nonequilibrium form. The characteristic functional of concentration fluctuations is evaluated in both cases by using the theory of random point processes. For large times the fluctuations of the concentration field are stationary and the corresponding probability density functional can be evaluated analytically. In this limit the fluctuations depend on the distribution of the total number of particles but are independent of the initial positions of the particles. We show that the logarithm of the stationary probability functional plays the role of a nonequilibrium thermodynamic potential, which has a structure similar to the Helmholtz free energy in equilibrium thermodynamics: it is made up of the sum of an energetic component, depending on the external mechanical potential, and of an entropic component, depending on

  14. Ensemble fits of restrained peptides' conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3.

    Science.gov (United States)

    Ciarkowski, Jerzy; Łuczak, Sylwia; Jagieła, Dawid; Sikorska, Emilia; Wójcik, Jacek; Oleszczuk, Marta; Izdebski, Jan

    2012-02-01

    Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr-D-Daa-Phe-Daa-NH₂ (Daa=diamino acid): 1 combining D-Dab² (α,γ-diaminobutyryl) with Lys⁴, and 2 -D-Dap² (α,β-diaminopropionyl) with Orn⁴. The ω-amino groups of D-Daa² and Daa⁴ are coupled with C=O into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and impotent μ/δ opioid peptides, respectively. To the current task, we took from an earlier work (Filip et al, J. Pept. Sci. 11 (2005) 347-352) the NMR NOE- and J-data in H₂O/D₂O; and the selection of the ensembles of 1 and 2, 822 and 788 conformational families, respectively, obtained by using the EDMC/ECEPP3 method. Here, we generated ensembles of 1 and 2 using AMBER molecular dynamics in explicit water to eventually selected 686 and 761 conformers for 1 and 2, respectively. We did numbers of fits for both types of the conformational ensembles of 1 and 2 to their NOE- and J-data using a common method i.e. maximum entropy approach (Groth et al, J. Biomol. NMR 15 (1999) 315-330). Both types of the well structurally diversified ensembles fit to quite different equilibria in regressions to common experimental NOE- and J-restraints using maximum entropy principle, which is a disappointing message. Intriguing is startlingly small standard deviation in J-couplings: σ(JNHαH) ≈ 0.01 Hz for LES-MD/AMBER ensemble, contrary to σ(JNHαH) = 0.8 - 1.1 Hz for the EDMC/ECEPP ensemble, over the wide range of entropy, i.e. relatively insensitive to it. A similar feature is not the case when comparing σ(NOE) in both methods. Hence, at minute entropy contributions, it follows that J does or does not transpose "overfitted" into the final σ(J) in the AMBER or ECEPP ensemble, respectively. Could this be an effect of softness of the AMBER flexible-valence force field compared to ECEPP rigid-geometry, and its effect on ensemble sampling? We do not know an

  15. Systematic parameter inference in stochastic mesoscopic modeling

    CERN Document Server

    Lei, Huan; Li, Zhen; Karniadakis, George

    2016-01-01

    We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are sparse. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space....

  16. Parameter Estimation

    DEFF Research Database (Denmark)

    2011-01-01

    of optimisation techniques coupled with dynamic solution of the underlying model. Linear and nonlinear approaches to parameter estimation are investigated. There is also the application of maximum likelihood principles in the estimation of parameters, as well as the use of orthogonal collocation to generate a set......In this chapter the importance of parameter estimation in model development is illustrated through various applications related to reaction systems. In particular, rate constants in a reaction system are obtained through parameter estimation methods. These approaches often require the application...... of algebraic equations as the basis for parameter estimation.These approaches are illustrated using estimations of kinetic constants from reaction system models....

  17. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

    Science.gov (United States)

    Joung, In Suk; Cheatham, Thomas E

    2009-10-01

    The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation-anion, water-cation, and water-anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali-halide salts were generally lower than the true solubility of the salts. However, for both the TIP4P(EW) and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion-ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4P(EW) water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.

  18. Articulatory Parameters.

    Science.gov (United States)

    Ladefoged, Peter

    1980-01-01

    Summarizes the 16 parameters hypothesized to be necessary and sufficient for linguistic phonetic specifications. Suggests seven parameters affecting tongue shapes, three determining the positions of the lips, one controlling the position of the velum, four varying laryngeal actions, and one controlling respiratory activity. (RL)

  19. Parameter Estimation

    DEFF Research Database (Denmark)

    Sales-Cruz, Mauricio; Heitzig, Martina; Cameron, Ian;

    2011-01-01

    of optimisation techniques coupled with dynamic solution of the underlying model. Linear and nonlinear approaches to parameter estimation are investigated. There is also the application of maximum likelihood principles in the estimation of parameters, as well as the use of orthogonal collocation to generate a set...

  20. Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting.

    Science.gov (United States)

    Margreitter, Christian; Oostenbrink, Chris

    2016-09-26

    Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken.

  1. Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

    Energy Technology Data Exchange (ETDEWEB)

    Morgado, Claudio A.; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jiri

    2009-06-09

    We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFTSAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle

  2. Inventory parameters

    CERN Document Server

    Sharma, Sanjay

    2017-01-01

    This book provides a detailed overview of various parameters/factors involved in inventory analysis. It especially focuses on the assessment and modeling of basic inventory parameters, namely demand, procurement cost, cycle time, ordering cost, inventory carrying cost, inventory stock, stock out level, and stock out cost. In the context of economic lot size, it provides equations related to the optimum values. It also discusses why the optimum lot size and optimum total relevant cost are considered to be key decision variables, and uses numerous examples to explain each of these inventory parameters separately. Lastly, it provides detailed information on parameter estimation for different sectors/products. Written in a simple and lucid style, it offers a valuable resource for a broad readership, especially Master of Business Administration (MBA) students.

  3. Development and evaluation of an automatically adjusting coarse-grained force field for a β-O-4 type lignin from atomistic simulations

    Science.gov (United States)

    Li, Wenzhuo; Zhao, Yingying; Huang, Shuaiyu; Zhang, Song; Zhang, Lin

    2017-01-01

    This goal of this work was to develop a coarse-grained (CG) model of a β-O-4 type lignin polymer, because of the time consuming process required to achieve equilibrium for its atomistic model. The automatic adjustment method was used to develop the lignin CG model, which enables easy discrimination between chemically-varied polymers. In the process of building the lignin CG model, a sum of n Gaussian functions was obtained by an approximation of the corresponding atomistic potentials derived from a simple Boltzmann inversion of the distributions of the structural parameters. This allowed the establishment of the potential functions of the CG bond stretching and angular bending. To obtain the potential function of the CG dihedral angle, an algorithm similar to a Fourier progression form was employed together with a nonlinear curve-fitting method. The numerical potentials of the nonbonded portion of the lignin CG model were obtained using a potential inversion iterative method derived from the corresponding atomistic nonbonded distributions. The study results showed that the proposed CG model of lignin agreed well with its atomistic model in terms of the distributions of bond lengths, bending angles, dihedral angles and nonbonded distances between the CG beads. The lignin CG model also reproduced the static and dynamic properties of the atomistic model. The results of the comparative evaluation of the two models suggested that the designed lignin CG model was efficient and reliable.

  4. Structural Properties of MgSiO3 Perovskite, Twin Walls and Their Binding to Oxygen Vacancies at High Pressures from Force Field Simulations

    Science.gov (United States)

    Goncalves-Ferreira, L.; Redfern, S. A.; Artacho, E.

    2007-12-01

    Aiming to understand possible origins of seismic wave attenuation and variations in the quality factor (Q) of minerals at the Earth's interior, it has been accepted that the friction in the motion of twin domain walls under applied stress leads to a reduction in Q [1]. To interpret this behaviour one must first appreciate the influence of pressure on wall motion and dynamics. Experimental observations of twin wall motion at high pressure are difficult at present. For this reason, we have undertaken a computational study of wall structure and dynamics in MgSiO3 perovskite, in the absence or presence of defects, as a function of pressure between 0 and 140 GPa. This work is based on previous studies on CaTiO3 perovskite [2,3] (symmetry Pbnm) with 7800 atoms and orthorhombic periodic boundary conditions. It has been geometrically adapted to lower mantle's MgSiO3 perovskite. The system comprises two (100) ferroelastic twin walls separated by 34.2 Å, relaxed within a variable supercell of 26x10x6 unit cells, with the rigid ion set of interatomic potentials with partial ionic charges employed by Alfredsson et al., 2005 [4]. The degree of distortion in the system is manifest in the octahedral tilting angles along each of the crystallographic directions. The octahedral tilting orientations close to the walls are well described by the behaviour of two order parameters: the main one, defining the wall, goes as α tanh(2(x - x')/w) , where α = 11.14° is the bulk value for the tilt, and w = 11.11 Å is the wall width. The secondary order parameters describe a slight breather at the wall. As wall dynamics are influenced by the presence of oxygen vacancies, we have calculated their binding energies to the described twin walls as a function of pressure. We find that this binding strongly depends on the vacancy disposition. For a vacancy between Si atoms in an axis perpendicular to the wall the binding energy is 1.09 eV at zero pressure. For vacancies along Si-Si axes parallel

  5. Dynamics of the [4Fe-4S] cluster in Pyrococcus furiosus D14C ferredoxin via nuclear resonance vibrational and resonance Raman spectroscopies, force field simulations, and density functional theory calculations.

    Science.gov (United States)

    Mitra, Devrani; Pelmenschikov, Vladimir; Guo, Yisong; Case, David A; Wang, Hongxin; Dong, Weibing; Tan, Ming-Liang; Ichiye, Toshiko; Jenney, Francis E; Adams, Michael W W; Yoda, Yoshitaka; Zhao, Jiyong; Cramer, Stephen P

    2011-06-14

    We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with (36)S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph(4)P)(2)[Fe(4)S(4)Cl(4)]. Several distinct regions of NRVS intensity are identified, ranging from "protein" and torsional modes below 100 cm(-1), through bending and breathing modes near 150 cm(-1), to strong bands from Fe-S stretching modes between 250 and ∼400 cm(-1). The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The (57)Fe partial vibrational densities of states for the oxidized samples were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low-frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe(4)S(4)](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.

  6. Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations

    Science.gov (United States)

    Mitra, Devrani; Pelmenschikov, Vladimir; Guo, Yisong; Case, David A.; Wang, Hongxin; Dong, Weibing; Tan, Ming-Liang; Ichiye, Toshiko; Jenney, Francis E.; Adams, Michael W. W.; Yoda, Yoshitaka; Zhao, Jiyong; Cramer, Stephen P.

    2011-01-01

    We have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal mode assignments, we recorded the NRVS of D14C ferredoxin samples with 36S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains: (Ph4P)2[Fe4S4Cl4]. Several distinct regions of NRVS intensity are identified, ranging from `protein' and torsional modes below 100 cm−1, through bending and breathing modes near 150 cm−1, to strong bands from Fe-S stretching modes between 250 cm−1 and ~400 cm−1. The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The 57Fe partial vibrational densities of states (PVDOS) for the oxidized samples were interpreted by normal mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe4S4]2+/1+ redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins. PMID:21500788

  7. Evaluation of the grand-canonical partition function using expanded Wang-Landau simulations. IV. Performance of many-body force fields and tight-binding schemes for the fluid phases of silicon.

    Science.gov (United States)

    Desgranges, Caroline; Delhommelle, Jerome

    2016-03-28

    We extend Expanded Wang-Landau (EWL) simulations beyond classical systems and develop the EWL method for systems modeled with a tight-binding Hamiltonian. We then apply the method to determine the partition function and thus all thermodynamic properties, including the Gibbs free energy and entropy, of the fluid phases of Si. We compare the results from quantum many-body (QMB) tight binding models, which explicitly calculate the overlap between the atomic orbitals of neighboring atoms, to those obtained with classical many-body (CMB) force fields, which allow to recover the tetrahedral organization in condensed phases of Si through, e.g., a repulsive 3-body term that favors the ideal tetrahedral angle. Along the vapor-liquid coexistence, between 3000 K and 6000 K, the densities for the two coexisting phases are found to vary significantly (by 5 orders of magnitude for the vapor and by up to 25% for the liquid) and to provide a stringent test of the models. Transitions from vapor to liquid are predicted to occur for chemical potentials that are 10%-15% higher for CMB models than for QMB models, and a ranking of the force fields is provided by comparing the predictions for the vapor pressure to the experimental data. QMB models also reveal the formation of a gap in the electronic density of states of the coexisting liquid at high temperatures. Subjecting Si to a nanoscopic confinement has a dramatic effect on the phase diagram with, e.g. at 6000 K, a decrease in liquid densities by about 50% for both CMB and QMB models and an increase in vapor densities between 90% (CMB) and 170% (QMB). The results presented here provide a full picture of the impact of the strategy (CMB or QMB) chosen to model many-body effects on the thermodynamic properties of the fluid phases of Si.

  8. Supergranular Parameters

    Science.gov (United States)

    Udayashankar, Paniveni

    2016-07-01

    I study the complexity of supergranular cells using intensity patterns from Kodaikanal solar observatory. The chaotic and turbulent aspect of the solar supergranulation can be studied by examining the interrelationships amongst the parameters characterizing supergranular cells namely size, horizontal flow field, lifetime and physical dimensions of the cells and the fractal dimension deduced from the size data. The findings are supportive of Kolmogorov's theory of turbulence. The Data consists of visually identified supergranular cells, from which a fractal dimension 'D' for supergranulation is obtained according to the relation P α AD/2 where 'A' is the area and 'P' is the perimeter of the supergranular cells. I find a fractal dimension close to about 1.3 which is consistent with that for isobars and suggests a possible turbulent origin. The cell circularity shows a dependence on the perimeter with a peak around (1.1-1.2) x 105 m. The findings are supportive of Kolmogorov's theory of turbulence.

  9. Calculation of the free energy of solvation for neutral analogs of amino acid side chains

    NARCIS (Netherlands)

    Villa, Alessandra; Mark, AE

    2002-01-01

    The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane

  10. Simulation study of the structure and phase behavior of ceramide bilayers and the role of lipid head group chemistry

    OpenAIRE

    Guo, Shan; Moore, Timothy C.; Iacovella, Christopher R.; Strickland, L. Anderson; McCabe, Clare

    2013-01-01

    Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field o...

  11. Simulation study of the structure and phase behavior of ceramide bilayers and the role of lipid head group chemistry

    OpenAIRE

    Guo, Shan; Moore, Timothy C.; Iacovella, Christopher R.; Strickland, L. Anderson; McCabe, Clare

    2013-01-01

    Ceramides are known to be a key component of the stratum corneum, the outermost protective layer of the skin that controls barrier function. In this work, molecular dynamics simulations are used to examine the behavior of ceramide bilayers, focusing on non-hydroxy sphingosine (NS) and non-hydroxy phytosphingosine (NP) ceramides. Here, we propose a modified version of the CHARMM force field for ceramide simulation, which is directly compared to the more commonly used GROMOS-based force field o...

  12. Crystal Structures from Nonempirical Force Fields

    Science.gov (United States)

    2008-01-01

    DELAWARE LIBRARY. Downloaded on September 14, 2009 at 19:17 from IEEE Xplore . Restrictions apply. component. Recently, a method has been developed...Authorized licensed use limited to: UNIVERSITY OF DELAWARE LIBRARY. Downloaded on September 14, 2009 at 19:17 from IEEE Xplore . Restrictions apply...limited to: UNIVERSITY OF DELAWARE LIBRARY. Downloaded on September 14, 2009 at 19:17 from IEEE Xplore . Restrictions apply. phenylalanine and FG

  13. DRF90 : a polarizable force field

    NARCIS (Netherlands)

    Swart, M.; van Duijnen, P. Th.

    2006-01-01

    The direct reaction field (DRF) approach has proven to be a useful tool to investigate the influence of solvents on the quantum/classical behaviour of solute molecules. In this paper, we report the latest extension of this DRF approach, which consists of the gradient of the completely classical ener

  14. Research on influencing factors of consolidation theory applicability in centrifugal force field%离心力场中固结理论适用性的影响因素研究

    Institute of Scientific and Technical Information of China (English)

    张莎莎; 谢永利

    2013-01-01

    为了明晰在较高的离心力场中,离心加速度及模型高度的变化对饱和土体固结理论适用性影响,提高离心力场中试验结果的可靠性,依据常规固结试验仪,研制了离心力场下的固结试验装置,并以此为基础,针对饱和砂土、典型海相土及河相土进行了不同离心力场下的固结模拟试验研究,同时对其试验时间与不同理论计算时间进行对比分析.结果表明,离心机模拟土体固结沉降时,离心加速度越大对总沉降量的影响也越大;在离心力场下,Terzaghi一维固结理论的应用有一定的局限性;不均匀离心力场和较高的模型高度对饱和土固结试验结果的影响较大,土体自重应予以考虑;现有离心模型试验的时间比尺应根据试验条件进行修正.%In order to research the impact of centrifugal model test results from the change of acceleration and the model height and improve the accuracy of centrifuge test results, based on conventional consolidation test instrument, The consolidation test device in centrifugal force field was developed. Taking the consolidation simulation of saturated sand, marine soil and saturated loess in different centrifugal acceleration field as subject, the comparison of test time and different theoretical computation time were analyzed. It is indicated that there are two phases in the consolidation process of saturated soil in centrifugal model test, namely the quick consolidation and the sequent slow consolidation. The quick consolidation process is mainly influenced by centrifugal acceleration. The application Terzaghi one-dimensional consolidation theory has its limitations in centrifugal force field. Uneven distribution and high of centrifugal acceleration on the model has a greater impact on the results, were the impact of soil weight must be considered. The existing time scale formula should be corrected by the test conditions.

  15. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

    Science.gov (United States)

    Liwo, Adam; Ołdziej, Stanisław; Czaplewski, Cezary; Kleinerman, Dana S; Blood, Philip; Scheraga, Harold A

    2010-03-09

    We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarse-grained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50 % efficiency and 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino-acid residues in days of wall-clock time.

  16. Parameters for Martini sterols and hopanoids based on a virtual-site description

    Science.gov (United States)

    Melo, M. N.; Ingólfsson, H. I.; Marrink, S. J.

    2015-12-01

    Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the use of virtual sites as a means of increasing the stability of cholesterol and cholesterol-like structures. We improve and extend the Martini parameterization of sterols in four different ways: 1—the cholesterol parameters were adapted to make use of virtual interaction sites, which markedly improves numerical stability; 2—cholesterol parameters were also modified to address reported shortcomings in reproducing correct lipid phase behavior in mixed membranes; 3—parameters for ergosterol were created and adapted from cholesterols; and 4—parameters for the hopanoid class of bacterial polycyclic molecules were created, namely, for hopane, diploptene, bacteriohopanetetrol, and for their polycyclic base structure.

  17. Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results.

    Science.gov (United States)

    Yildirim, Ilyas; Kierzek, Elzbieta; Kierzek, Ryszard; Schatz, George C

    2014-12-11

    When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both

  18. Achieving High Accuracy in Calculations of NMR Parameters

    DEFF Research Database (Denmark)

    Faber, Rasmus

    , the (aug-)pcJ-n, n=1,2,3 and the (aug-)ccJpVXZ, X=D,T,Q,5, have been compared for systems where both contact and non-contact contributions to the SSCC are important. It was found that the triple zeta basis sets with diffuse functions, i.e. aug-ccJ-pVTZ or augpcJ- 2, can provide well converged results...... calculations is split amongst errors in the molecular force-field parameters and errors in the shielding surface. Finally, accurate vibrational corrections to the nuclear shielding calculations of noble-gas dimers are presented. While these corrections are small compared to the total shielding, they have...

  19. Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase.

    Science.gov (United States)

    Sovová, Žofie; Berka, Karel; Otyepka, Michal; Jurečka, Petr

    2015-03-12

    Ceramides are lipids that are involved in numerous biologically important structures (e.g., the stratum corneum and ceramide-rich platforms) and processes (e.g., signal transduction and membrane fusion), but their behavior is not fully understood. We report coarse-grain force field parameters for N-lignocerylsphingosine (ceramide NS, also known as ceramide 2) that are consistent with the Martini force field. These parameters were optimized for simulations in the gel phase and validated against atomistic simulations. Coarse-grained simulations with our parameters provide areas per lipid, membrane thicknesses, and electron density profiles that are in good agreement with atomistic simulations. Properties of the simulated membranes are compared with available experimental data. The obtained parameters were used to model the phase behavior of ceramide NS as a function of temperature and hydration. At low water content and above the main phase transition temperature, the bilayer melts into an irregular phase, which may correspond to the unstructured melted-chain phase observed in X-ray diffraction experiments. The developed parameters also reproduce the extended conformation of ceramide, which may occur in the stratum corneum. The parameters presented herein will facilitate studies on important complex functional structures such as the uppermost layer of the skin and ceramide-rich platforms in phospholipid membranes.

  20. Dynamics of an [Fe{sub 4}S{sub 4}(SPh){sub 4}{sup 2-} cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using {sup 36}S substitution, DFT calculations, and empirical force fields.

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Y.; Koutmos, M.; Case, D.A.; Coucouvanis, D.; Wang, H.; Cramer, S.P.; X-Ray Science Division; Univ. of California; LBNL; The Scripps Research Inst.; Univ. of Michigan

    2006-01-01

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and {sup 57}Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu){sub 4}N]{sub 2}[Fe{sub 4}S{sub 4}(SPh){sub 4}]. This [Fe{sub 4}S{sub 4}(SR){sub 4}]{sup 2-} complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with {sup 36}S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies.The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after {sup 36}S substitution were used as an additional constraint. A D{sub 2d} symmetry Fe{sub 4}S{sub 4}S{sub 4} model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D{sub 2d} Fe{sub 4}S{sub 4}(SPh){sub 4} model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between 50 and 100 cm{sup -1} were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe{sub 4}S{sub 4} cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to rotational lattice modes. We also reassign the 430 cm{sup -1} band as primarily an elongation of the thiophenolate ring, with 10% terminal Fe-S stretch character. This study illustrates the

  1. Simulation of carbohydrates, from molecular docking to dynamics in water.

    Science.gov (United States)

    Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

    2013-01-01

    Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

  2. 基于CHARMM力场的蛋白质分子场计算及触觉感知%Computation and Haptic Application of Protein Interaction Fields Based on CHARMM Force Field

    Institute of Scientific and Technical Information of China (English)

    汪莉; 万华根; 彭群生

    2009-01-01

    分子场是研究分子结构与功能的重要工具之一,已经成为药物设计和分子对接的常规方法.由于触觉设备能提供丰富的感官信息,近年来触觉交互正逐渐成为该领域的研究热点.文中研究了蛋白质分子场的触觉感知.首先从蛋白质分子结构出发,基于CHARMM力场,经过分子动力学模拟采样计算得到蛋白质分子场;然后结合触觉设备建立触觉感知模型,通过视觉与触觉相结合的方式分析分子场能量分布以丰富分子场的感知信息;最后绘制触觉场景并给用户提供相关的视觉和触觉反馈.实验结果表明,文中提出的分子场计算方法鲁棒,且触觉系统能保持较好的稳定性.%Molecular interaction field (MIF) is an important tool for studying the intrinsic relationship between molecular structure and function. It has been established as a conventional method in rational drug design and molecular docking. MIF can be experienced by user through a haptic device. In this paper, the haptic application of protein interaction fields is investigated. The MIF is constructed based on the macromolecular structure of a protein by computing the molecular dynamics with the CHARMM force field. Then a haptic perceptual model is developed with which the MIF energy distribution is analyzed both visually and haptically to afford much richer sensational information. Finally, the haptic scene is rendered and the resultant force is delivered to the user. Experimental statistics show that the proposed MIF computation method is robust with stable haptic feedback.

  3. Reversible and Irreversible Adsorption Energetics of Poly(ethylene glycol) and Sorbitan Poly(ethoxylate) at a Water/Alkane Interface.

    Science.gov (United States)

    Huston, Kyle J; Larson, Ronald G

    2015-07-14

    We simulate poly(ethylene glycol) (PEG) oligomers and model Tween 80 (polyoxyethylene sorbitan monooleate) molecules at water/alkane interfaces. Using the weighted histogram analysis method (WHAM), including an extension of WHAM to two reaction coordinates to remove hysteresis, we calculate interfacial potentials of mean force (PMFs) for PEG and Tween 80 using three force fields: the atomistic GROMOS 53a6OXY+D and two coarse-grained (CG) MARTINI force fields. Because the force fields have not yet been validated for PEO adsorption to hydrophobic interfaces, we calculate PMFs for alcohol ethoxylates C12E2 and C12E8 and find that they agree with semiempirical results of Mulqueen and Blankschtein [Langmuir 2002, 18 (2), 365-376] for the GROMOS 53a6OXY+D force field, whereas for both MARTINI force fields, PEO adsorbs too weakly to a clean hydrophobic interface. One MARTINI force field incorrectly shows depletion rather than adsorption to a clean hydrophobic interface. We find that the adsorption free energy for PEG oligomers at a clean, planar water/alkane interface is around 1.3 kBT per monomer for the atomistic force field but is less than half of this for the two CG force fields. With the newly validated GROMOS 53a6OXY+D force field, we bracket the dilute adsorption free energy for a model Tween 80 molecule at the clean water/squalane interface. We also calculate the pressure-area isotherm. We exploit these data with the Nikas-Mulqueen-Blankschtein (NMB) theory and a simple transport model to demonstrate a transition from irreversible to reversible adsorption with increasing surface coverage, consistent with experimental results of Reichert and Walker [Langmuir 2013, 29 (6), 1857-1867].

  4. Force-field functor theory: classical force-fields which reproduce equilibrium quantum distributions.

    Science.gov (United States)

    Babbush, Ryan; Parkhill, John; Aspuru-Guzik, Alán

    2013-01-01

    Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory.

  5. Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives

    Directory of Open Access Journals (Sweden)

    Francisco Torrens

    2009-03-01

    Full Text Available The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use of additive values for atom polarizabilities gives poor results, in some cases leading to artificial predictions of absorption bands. The molecular polarizability of methane and its derivative are computed. The agreement with experimental mean molecular polarizabilities is within 1–5%. A hypothesis is indispensable for a suitable representation of polarizability derivative.

  6. Force-Field Functor Theory: Classical Force-Fields which Reproduce Equilibrium Quantum Distributions

    Directory of Open Access Journals (Sweden)

    Ryan eBabbush

    2013-10-01

    Full Text Available Feynman and Hibbs were the first to variationally determine an effective potential whose associated classical canonical ensemble approximates the exact quantum partition function. We examine the existence of a map between the local potential and an effective classical potential which matches the exact quantum equilibrium density and partition function. The usefulness of such a mapping rests in its ability to readily improve Born-Oppenheimer potentials for use with classical sampling. We show that such a map is unique and must exist. To explore the feasibility of using this result to improve classical molecular mechanics, we numerically produce a map from a library of randomly generated one-dimensional potential/effective potential pairs then evaluate its performance on independent test problems. We also apply the map to simulate liquid para-hydrogen, finding that the resulting radial pair distribution functions agree well with path integral Monte Carlo simulations. The surprising accessibility and transferability of the technique suggest a quantitative route to adapting Born-Oppenheimer potentials, with a motivation similar in spirit to the powerful ideas and approximations of density functional theory.

  7. Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions

    CERN Document Server

    Mao, Albert H; 10.1063/1.4742068

    2012-01-01

    Accurate models of alkali and halide ions in aqueous solution are necessary for computer simulations of a broad variety of systems. Previous efforts to develop ion force fields have generally focused on reproducing experimental measurements of aqueous solution properties such as hydration free energies and ion-water distribution functions. This dependency limits transferability of the resulting parameters because of the variety and known limitations of water models. We present a solvent-independent approach to calibrating ion parameters based exclusively on crystal lattice properties. Our procedure relies on minimization of lattice sums to calculate lattice energies and interionic distances instead of equilibrium ensemble simulations of dense fluids. The gain in computational efficiency enables simultaneous optimization of all parameters for Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I- subject to constraints that enforce consistency with periodic table trends. We demonstrate the method by presenting lattice-d...

  8. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.

    Science.gov (United States)

    Margreitter, Christian; Petrov, Drazen; Zagrovic, Bojan

    2013-07-01

    Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package.

  9. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

    Science.gov (United States)

    Margreitter, Christian; Petrov, Drazen; Zagrovic, Bojan

    2013-01-01

    Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package. PMID:23703210

  10. Lumped-parameter models

    Energy Technology Data Exchange (ETDEWEB)

    Ibsen, Lars Bo; Liingaard, M.

    2006-12-15

    A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. In this technical report the steps of establishing a lumped-parameter model are presented. Following sections are included in this report: Static and dynamic formulation, Simple lumped-parameter models and Advanced lumped-parameter models. (au)

  11. Redefining solubility parameters: the partial solvation parameters.

    Science.gov (United States)

    Panayiotou, Costas

    2012-03-21

    The present work reconsiders a classical and universally accepted concept of physical chemistry, the solubility parameter. Based on the insight derived from modern quantum chemical calculations, a new definition of solubility parameter is proposed, which overcomes some of the inherent restrictions of the original definition and expands its range of applications. The original single solubility parameter is replaced by four partial solvation parameters reflecting the dispersion, the polar, the acidic and the basic character of the chemical compounds as expressed either in their pure state or in mixtures. Simple rules are adopted for the definition and calculation of these four parameters and their values are tabulated for a variety of common substances. In contrast, however, to the well known Hansen solubility parameters, their design and evaluation does not rely exclusively on the basic rule of "similarity matching" for solubility but it makes also use of the other basic rule of compatibility, namely, the rule of "complementarity matching". This complementarity matching becomes particularly operational with the sound definition of the acidic and basic components of the solvation parameter based on the third σ-moments of the screening charge distributions of the quantum mechanics-based COSMO-RS theory. The new definitions are made in a simple and straightforward manner, thus, preserving the strength and appeal of solubility parameter stemming from its simplicity. The new predictive method has been applied to a variety of solubility data for systems of pharmaceuticals and polymers. The results from quantum mechanics calculations are critically compared with the results from Abraham's acid/base descriptors.

  12. Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations.

    Science.gov (United States)

    Kaukonen, M; Gulans, A; Havu, P; Kauppinen, E

    2012-03-05

    Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential.

  13. Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

    Science.gov (United States)

    Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

    2015-12-28

    Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

  14. Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

    Science.gov (United States)

    Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

    2012-01-01

    The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

  15. Estimating Cosmological Parameter Covariance

    CERN Document Server

    Taylor, Andy

    2014-01-01

    We investigate the bias and error in estimates of the cosmological parameter covariance matrix, due to sampling or modelling the data covariance matrix, for likelihood width and peak scatter estimators. We show that these estimators do not coincide unless the data covariance is exactly known. For sampled data covariances, with Gaussian distributed data and parameters, the parameter covariance matrix estimated from the width of the likelihood has a Wishart distribution, from which we derive the mean and covariance. This mean is biased and we propose an unbiased estimator of the parameter covariance matrix. Comparing our analytic results to a numerical Wishart sampler of the data covariance matrix we find excellent agreement. An accurate ansatz for the mean parameter covariance for the peak scatter estimator is found, and we fit its covariance to our numerical analysis. The mean is again biased and we propose an unbiased estimator for the peak parameter covariance. For sampled data covariances the width estimat...

  16. Lumped-parameter models

    DEFF Research Database (Denmark)

    Ibsen, Lars Bo; Liingaard, Morten

    A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. The lumped-parameter model development have been reported by (Wolf 1991b; Wolf 1991a; Wolf and Paronesso 1991; Wolf and Paronesso 19...

  17. 1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies.

    Science.gov (United States)

    Garrido, Nuno M; Queimada, António J; Jorge, Miguel; Macedo, Eugénia A; Economou, Ioannis G

    2009-09-08

    The 1-octanol/water partition coefficient is an important thermodynamic variable usually employed to understand and quantify the partitioning of solutes between aqueous and organic phases. It finds widespread use in many empirical correlations to evaluate the environmental fate of pollutants as well as in the design of pharmaceuticals. The experimental evaluation of 1-octanol/water partition coefficients is an expensive and time-consuming procedure, and thus, theoretical estimation methods are needed, particularly when a physical sample of the solute may not yet be available, such as in pharmaceutical screening. 1-Octanol/water partition coefficients can be obtained from Gibbs free energies of solvation of the solute in both the aqueous and the octanol phases. The accurate evaluation of free energy differences remains today a challenging problem in computational chemistry. In order to study the absolute solvation Gibbs free energies in 1-octanol, a solvent that can mimic many properties of important biological systems, free energy calculations for n-alkanes in the range C1-C8 were performed using molecular simulation techniques, following the thermodynamic integration approach. In the first part of this paper, we test different force fields by evaluating their performance in reproducing pure 1-octanol properties. It is concluded that all-atom force fields can provide good accuracy but at the cost of a higher computational time compared to that of the united-atom force fields. Recent versions of united-atom force fields, such as Gromos and TraPPE, provide satisfactory results and are, thus, useful alternatives to the more expensive all-atom models. In the second part of the paper, the Gibbs free energy of solvation in 1-octanol is calculated for several n-alkanes using three force fields to describe the solutes, namely Gromos, TraPPE, and OPLS-AA. Generally, the results obtained are in excellent agreement with the available experimental data and are of similar

  18. A new approach to electron diffraction analysis of symmetric triatomic molecules with large-amplitude bending motion : The equilibrium geometry, force field and vibrational frequencies of BaI2 as determined by electron diffraction

    Science.gov (United States)

    Spiridonov, V. P.; Gershikov, A. G.; Altman, A. B.; Romanov, G. V.; Ivanov, A. A.

    1981-01-01

    Diffraction data on BaI 2, analyzed by a new approach, indicate an anharmonic potential with a barrier of 71(12) cm -1 at a linear geometry. The structural and vibrational parameters were found to be reh(Ba-I o) = 3.150(7)Å, ∠ eIBaI = 148.0(9) °, fq = 0.69(8) mdyn/Å, fqq= 0.14(6) mdyn/Å, k2 = -0.0075(15) mdyn/Å, k4 = 0.0025(9) mdyn/Å 3, v1 = 106(12) cm -1 and v3 = 145(21) cm -1. The bending frequency v2 is predicted to be near 16 cm -1.

  19. Supersymmetry Parameter Analysis

    CERN Document Server

    Kalinowski, Jan

    2002-01-01

    Supersymmetric particles can be produced copiously at future colliders. From the high-precision data taken at e+e- linear colliders, TESLA in particular, and combined with results from LHC, and CLIC later, the low-energy parameters of the supersymmetric model can be determined. Evolving the parameters from the low-energy scale to the high-scale by means of renormalization group techniques the fundamental supersymmetry parameters at the high scale, GUT or Planck, can be reconstructed to reveal the origin of supersymmetry breaking.

  20. Magnetic S-parameter

    DEFF Research Database (Denmark)

    Sannino, Francesco

    2010-01-01

    We propose a direct test of the existence of gauge duals for nonsupersymmetric asymptotically free gauge theories developing an infrared fixed point by computing the S-parameter in the electric and dual magnetic description. In particular we show that at the lower bound of the conformal window...... the magnetic S-parameter, i.e. the one determined via the dual magnetic gauge theory, assumes a simple expression in terms of the elementary magnetic degrees of freedom. The results further support our recent conjecture of the existence of a universal lower bound on the S parameter and indicates...

  1. Revisiting Cosmological parameter estimation

    CERN Document Server

    Prasad, Jayanti

    2014-01-01

    Constraining theoretical models with measuring the parameters of those from cosmic microwave background (CMB) anisotropy data is one of the most active areas in cosmology. WMAP, Planck and other recent experiments have shown that the six parameters standard $\\Lambda$CDM cosmological model still best fits the data. Bayesian methods based on Markov-Chain Monte Carlo (MCMC) sampling have been playing leading role in parameter estimation from CMB data. In one of the recent studies \\cite{2012PhRvD..85l3008P} we have shown that particle swarm optimization (PSO) which is a population based search procedure can also be effectively used to find the cosmological parameters which are best fit to the WMAP seven year data. In the present work we show that PSO not only can find the best-fit point, it can also sample the parameter space quite effectively, to the extent that we can use the same analysis pipeline to process PSO sampled points which is used to process the points sampled by Markov Chains, and get consistent res...

  2. Parameter Estimation Through Ignorance

    CERN Document Server

    Du, Hailiang

    2015-01-01

    Dynamical modelling lies at the heart of our understanding of physical systems. Its role in science is deeper than mere operational forecasting, in that it allows us to evaluate the adequacy of the mathematical structure of our models. Despite the importance of model parameters, there is no general method of parameter estimation outside linear systems. A new relatively simple method of parameter estimation for nonlinear systems is presented, based on variations in the accuracy of probability forecasts. It is illustrated on the Logistic Map, the Henon Map and the 12-D Lorenz96 flow, and its ability to outperform linear least squares in these systems is explored at various noise levels and sampling rates. As expected, it is more effective when the forecast error distributions are non-Gaussian. The new method selects parameter values by minimizing a proper, local skill score for continuous probability forecasts as a function of the parameter values. This new approach is easier to implement in practice than alter...

  3. MSSM without free parameters

    Science.gov (United States)

    Kitano, Ryuichiro; Motono, Ryuji; Nagai, Minoru

    2016-12-01

    It is often argued that the minimal supersymmetric standard model has O (100 ) free parameters, and the generic parameter region is already excluded by the null observation of the flavor and C P -violating processes as well as the constraints from the LHC experiments. This situation naturally leads us to consider the case where all the dangerous soft supersymmetry breaking terms, such as the scalar masses and scalar couplings, are absent, while only the unified gaugino mass term and the μ term are nonvanishing at the grand unification scale. We revisit this simple situation taking into account the observed Higgs boson mass, 125 GeV. Since the gaugino mass and the μ term are fixed in order to explain the Higgs boson and the Z boson masses, there is no free parameter left in this scenario. We find that there are three independent parameter sets that exist including ones which have not been discussed in the literature. We also find that the abundance of the dark matter can be explained by relic gravitinos which are nonthermally produced as decay products of the supersymmetry particles while satisfying constraints from big bang nucleosynthesis. We discuss the effects of the gravity mediation which generically gives a contribution to the soft terms of the order of the gravitino mass. It turns out that a newly found parameter set is preferable to explain the Higgs boson mass as well as the gravitino dark matter while satisfying the constraints from the electric dipole moments of the electron and the nucleon.

  4. Refinements of water parameters for molecular dynamics: Simulations of adsorption at the clay mineral/aqueous solution interface

    DEFF Research Database (Denmark)

    Schäfer, L.; Yu, C.; Teppen, B.J.;

    1999-01-01

    In the context of a long-term program involving molecular dynamics simulations of adsorption phenomena at the clay mineral/aqueous solution interface, we are testing the viability of combining a force field that we developed specificially for clays with other, independently derived potential...... parameters for molecular species which are important in clay adsorption. For the current study the importance of variations in the potential parameters of water were investigated and polarization effects on oxygen studied as a function of intermolecular interactions. For this purpose ab initio MP2/6-311GG...... atomic charges were determined for several oligomers of water and for the water dimer at different intermolecular separations. Charge variations of up to ~0.1 electron charge unit on oxygen are found and, together with changes in van der Waals constants, their significance for dynamics simulations...

  5. Fundamental stellar parameters

    CERN Document Server

    Wittkowski, M

    2004-01-01

    I present a discussion of fundamental stellar parameters and their observational determina