Literature DB >> 35507313

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

Simon Boothroyd1,2, Lee-Ping Wang3, David L Mobley4, John D Chodera1, Michael R Shirts2.   

Abstract

Developing accurate classical force field representations of molecules is key to realizing the full potential of molecular simulations, both as a powerful route to gaining fundamental insights into a broad spectrum of chemical and biological phenomena and for predicting physicochemical and mechanical properties of substances. The Open Force Field Consortium is an industry-funded open science effort to this end, developing open-source tools for rapidly generating new high-quality small-molecule force fields. An integral aspect of this is the parameterization and assessment of force fields against high-quality, condensed-phase physical property data, curated from open data sources such as the NIST ThermoML Archive, alongside quantum chemical data. The quantity of such experimental data in open data archives alone would require an onerous amount of human and computational resources to both curate and estimate manually, especially when estimations must be obtained for numerous sets of force field parameters. Here, we present an entirely automated, highly scalable framework for evaluating physical properties and their gradients in terms of force field parameters. It is written as a modular and extensible Python framework, which employs an intelligent multiscale estimation approach that allows for the automated estimation of properties from simulation and cached simulation data, and a pluggable API for estimation of new properties. In this study, we demonstrate the utility of the framework by benchmarking the OpenFF 1.0.0 small-molecule force field and GAFF 1.8 and GAFF 2.1 force fields against a test set of binary density and enthalpy of mixing measurements curated using the framework utilities. Further, we demonstrate the framework's utility as part of force field optimization by using it alongside ForceBalance, a framework for systematic force field optimization, to retrain a set of nonbonded van der Waals parameters against a training set of density and enthalpy of vaporization measurements.

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Year:  2022        PMID: 35507313      PMCID: PMC9245177          DOI: 10.1021/acs.jctc.1c01111

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


  19 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.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

3.  Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data.

Authors:  Lee-Ping Wang; Jiahao Chen; Troy Van Voorhis
Journal:  J Chem Theory Comput       Date:  2012-11-29       Impact factor: 6.006

4.  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

5.  Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

Authors:  Hans W Horn; William C Swope; Jed W Pitera
Journal:  J Chem Phys       Date:  2005-11-15       Impact factor: 3.488

6.  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

7.  FreeSolv: a database of experimental and calculated hydration free energies, with input files.

Authors:  David L Mobley; J Peter Guthrie
Journal:  J Comput Aided Mol Des       Date:  2014-06-14       Impact factor: 3.686

8.  Systematic Optimization of Water Models Using Liquid/Vapor Surface Tension Data.

Authors:  Yudong Qiu; Paul S Nerenberg; Teresa Head-Gordon; Lee-Ping Wang
Journal:  J Phys Chem B       Date:  2019-07-31       Impact factor: 2.991

9.  Systematic improvement of a classical molecular model of water.

Authors:  Lee-Ping Wang; Teresa Head-Gordon; Jay W Ponder; Pengyu Ren; John D Chodera; Peter K Eastman; Todd J Martinez; Vijay S Pande
Journal:  J Phys Chem B       Date:  2013-08-14       Impact factor: 2.991

10.  Optimized Lennard-Jones Parameters for Druglike Small Molecules.

Authors:  Eliot Boulanger; Lei Huang; Chetan Rupakheti; Alexander D MacKerell; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2018-05-07       Impact factor: 6.006

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  1 in total

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

Authors:  Simon Boothroyd; Owen C Madin; David L Mobley; Lee-Ping Wang; John D Chodera; Michael R Shirts
Journal:  J Chem Theory Comput       Date:  2022-05-09       Impact factor: 6.578

  1 in total

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