Literature DB >> 26589047

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data.

Lee-Ping Wang1, Jiahao Chen2, Troy Van Voorhis2.   

Abstract

We introduce ForceBalance, a method and free software package for systematic force field optimization with the ability to parametrize a wide variety of functional forms using flexible combinations of reference data. We outline several important challenges in force field development and how they are addressed in ForceBalance, and present an example calculation where these methods are applied to develop a highly accurate polarizable water model. ForceBalance is available for free download at https://simtk.org/home/forcebalance.

Entities:  

Year:  2012        PMID: 26589047     DOI: 10.1021/ct300826t

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  49 in total

1.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

2.  Variational cross-validation of slow dynamical modes in molecular kinetics.

Authors:  Robert T McGibbon; Vijay S Pande
Journal:  J Chem Phys       Date:  2015-03-28       Impact factor: 3.488

Review 3.  Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.

Authors:  J V Vermaas; N Trebesch; C G Mayne; S Thangapandian; M Shekhar; P Mahinthichaichan; J L Baylon; T Jiang; Y Wang; M P Muller; E Shinn; Z Zhao; P-C Wen; E Tajkhorshid
Journal:  Methods Enzymol       Date:  2016-07-11       Impact factor: 1.600

4.  Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Authors:  Kyle A Beauchamp; Vijay S Pande; Rhiju Das
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

5.  Robustness in the fitting of molecular mechanics parameters.

Authors:  Kenno Vanommeslaeghe; Mingjun Yang; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2015-03-31       Impact factor: 3.376

6.  Data-driven analysis of the number of Lennard-Jones types needed in a force field.

Authors:  Michael Schauperl; Sophie Kantonen; Lee-Ping Wang; Michael K Gilson
Journal:  Commun Chem       Date:  2020-11-13

7.  Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Authors:  Marie L Laury; Lee-Ping Wang; Vijay S Pande; Teresa Head-Gordon; Jay W Ponder
Journal:  J Phys Chem B       Date:  2015-02-26       Impact factor: 2.991

8.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

9.  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

10.  United polarizable multipole water model for molecular mechanics simulation.

Authors:  Rui Qi; Lee-Ping Wang; Qiantao Wang; Vijay S Pande; Pengyu Ren
Journal:  J Chem Phys       Date:  2015-07-07       Impact factor: 3.488

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