Literature DB >> 35129974

Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models.

Owen C Madin1, Simon Boothroyd2, Richard A Messerly3, Josh Fass4, John D Chodera5, Michael R Shirts1.   

Abstract

A high level of physical detail in a molecular model improves its ability to perform high accuracy simulations but can also significantly affect its complexity and computational cost. In some situations, it is worthwhile to add complexity to a model to capture properties of interest; in others, additional complexity is unnecessary and can make simulations computationally infeasible. In this work, we demonstrate the use of Bayesian inference for molecular model selection, using Monte Carlo sampling techniques accelerated with surrogate modeling to evaluate the Bayes factor evidence for different levels of complexity in the two-centered Lennard-Jones + quadrupole (2CLJQ) fluid model. Examining three nested levels of model complexity, we demonstrate that the use of variable quadrupole and bond length parameters in this model framework is justified only for some chemistries. Through this process, we also get detailed information about the distributions and correlation of parameter values, enabling improved parametrization and parameter analysis. We also show how the choice of parameter priors, which encode previous model knowledge, can have substantial effects on the selection of models, penalizing careless introduction of additional complexity. We detail the computational techniques used in this analysis, providing a roadmap for future applications of molecular model selection via Bayesian inference and surrogate modeling.

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Year:  2022        PMID: 35129974      PMCID: PMC9217127          DOI: 10.1021/acs.jcim.1c00829

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   6.162


  35 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.  Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

Authors:  John D Chodera; Michael R Shirts
Journal:  J Chem Phys       Date:  2011-11-21       Impact factor: 3.488

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

Authors:  S Wu; P Angelikopoulos; C Papadimitriou; R Moser; P Koumoutsakos
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-02-13       Impact factor: 4.226

4.  ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept.

Authors:  Michael Frenkel; Robert D Chirico; Vladimir Diky; Xinjian Yan; Qian Dong; Chris Muzny
Journal:  J Chem Inf Model       Date:  2005 Jul-Aug       Impact factor: 4.956

5.  Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint.

Authors:  Sergio Bacallado; John D Chodera; Vijay Pande
Journal:  J Chem Phys       Date:  2009-07-28       Impact factor: 3.488

6.  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

7.  Current status of the AMOEBA polarizable force field.

Authors:  Jay W Ponder; Chuanjie Wu; Pengyu Ren; Vijay S Pande; John D Chodera; Michael J Schnieders; Imran Haque; David L Mobley; Daniel S Lambrecht; Robert A DiStasio; Martin Head-Gordon; Gary N I Clark; Margaret E Johnson; Teresa Head-Gordon
Journal:  J Phys Chem B       Date:  2010-03-04       Impact factor: 2.991

8.  A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes.

Authors:  See-Wing Chiu; H Larry Scott; Eric Jakobsson
Journal:  J Chem Theory Comput       Date:  2010-02-17       Impact factor: 6.006

Review 9.  SciPy 1.0: fundamental algorithms for scientific computing in Python.

Authors:  Pauli Virtanen; Ralf Gommers; Travis E Oliphant; Matt Haberland; Tyler Reddy; David Cournapeau; Evgeni Burovski; Pearu Peterson; Warren Weckesser; Jonathan Bright; Stéfan J van der Walt; Matthew Brett; Joshua Wilson; K Jarrod Millman; Nikolay Mayorov; Andrew R J Nelson; Eric Jones; Robert Kern; Eric Larson; C J Carey; İlhan Polat; Yu Feng; Eric W Moore; Jake VanderPlas; Denis Laxalde; Josef Perktold; Robert Cimrman; Ian Henriksen; E A Quintero; Charles R Harris; Anne M Archibald; Antônio H Ribeiro; Fabian Pedregosa; Paul van Mulbregt
Journal:  Nat Methods       Date:  2020-02-03       Impact factor: 28.547

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