Literature DB >> 35533269

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties.

Simon Boothroyd1, Owen C Madin2, David L Mobley3,4, Lee-Ping Wang5, John D Chodera6, Michael R Shirts2.   

Abstract

Developing a sufficiently accurate classical force field representation of molecules is key to realizing the full potential of molecular simulations as a route to gaining a fundamental insight into a broad spectrum of chemical and biological phenomena. This is only possible, however, if the many complex interactions between molecules of different species in the system are accurately captured by the model. Historically, the intermolecular van der Waals (vdW) interactions have primarily been trained against densities and enthalpies of vaporization of pure (single-component) systems, with occasional usage of hydration free energies. In this study, we demonstrate how including physical property data of binary mixtures can better inform these parameters, encoding more information about the underlying physics of the system in complex chemical mixtures. To demonstrate this, we retrain a select number of Lennard-Jones parameters describing the vdW interactions of the OpenFF 1.0.0 (Parsley) fixed charge force field against training sets composed of densities and enthalpies of mixing for binary liquid mixtures as well as densities and enthalpies of vaporization of pure liquid systems and assess the performance of each of these combinations. We show that retraining against the mixture data improves the force field's ability to reproduce mixture properties, including solvation free energies, correcting some systematic errors that exist when training vdW interactions against properties of pure systems only.

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Year:  2022        PMID: 35533269      PMCID: PMC9254460          DOI: 10.1021/acs.jctc.1c01268

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.578


  33 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Building Force Fields: An Automatic, Systematic, and Reproducible Approach.

Authors:  Lee-Ping Wang; Todd J Martinez; Vijay S Pande
Journal:  J Phys Chem Lett       Date:  2014-05-16       Impact factor: 6.475

3.  PACKMOL: a package for building initial configurations for molecular dynamics simulations.

Authors:  L Martínez; R Andrade; E G Birgin; J M Martínez
Journal:  J Comput Chem       Date:  2009-10       Impact factor: 3.376

4.  Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach.

Authors:  Martin Stroet; Katarzyna B Koziara; Alpeshkumar K Malde; Alan E Mark
Journal:  J Chem Theory Comput       Date:  2017-11-21       Impact factor: 6.006

5.  Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters.

Authors:  Sophie M Kantonen; Hari S Muddana; Michael Schauperl; Niel M Henriksen; Lee-Ping Wang; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2020-01-17       Impact factor: 6.006

6.  Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds.

Authors:  I Jen Chen; Daxu Yin; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2002-01-30       Impact factor: 3.376

7.  Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation.

Authors:  Simon Boothroyd; Lee-Ping Wang; David L Mobley; John D Chodera; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2022-05-04       Impact factor: 6.578

8.  Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Authors:  David L Mobley; Caitlin C Bannan; Andrea Rizzi; Christopher I Bayly; John D Chodera; Victoria T Lim; Nathan M Lim; Kyle A Beauchamp; David R Slochower; Michael R Shirts; Michael K Gilson; Peter K Eastman
Journal:  J Chem Theory Comput       Date:  2018-10-30       Impact factor: 6.006

9.  Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

Authors:  Kai Wang; John D Chodera; Yanzhi Yang; Michael R Shirts
Journal:  J Comput Aided Mol Des       Date:  2013-12-03       Impact factor: 3.686

10.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

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  1 in total

1.  Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation.

Authors:  Simon Boothroyd; Lee-Ping Wang; David L Mobley; John D Chodera; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2022-05-04       Impact factor: 6.578

  1 in total

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