Literature DB >> 30113842

Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties.

Alexander D Wade1, Lee-Ping Wang2, David J Huggins1,3,4.   

Abstract

The structural properties of three- and four-site water models are improved by extending the ForceBalance parametrization code to include a new methodology allowing for the targeting of any radial distribution function (RDF) during the parametrization of a force field. The mean squared difference (MSD) between the experimental and simulated RDFs contributes to an objective function, allowing for the systematic optimization of force field parameters to reach closer overall agreement with experiment. RDF fitting is applied to develop modified versions of the TIP3P and TIP4P/2005 water models in which the Lennard-Jones potential is replaced by a Buckingham potential. The optimized TIP3P-Buckingham and TIP4P-Buckingham potentials feature 93 and 98% lower MSDs in the OO RDF compared to the TIP3P and TIP4P/2005 models respectively, with marked decreases in the height of the first peak. Additionally, these Buckingham models predict the entropy of water more accurately, reducing the error in the entropy of TIP3P from 11 to 3% and the error in the entropy of TIP4P/2005 from 11 to 2%. These new Buckingham models have improved predictive power for many nonfitted properties particularly in the case of TIP3P. Our work directly demonstrates how the Buckingham potential can improve the description of water's structural properties beyond the Lennard-Jones potential. Moreover, adding a Buckingham potential is a favorable alternative to adding interaction sites in terms of computational speed on modern GPU hardware.

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Year:  2018        PMID: 30113842      PMCID: PMC6175054          DOI: 10.1021/acs.jcim.8b00166

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  24 in total

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Journal:  J Chem Phys       Date:  2004-04-01       Impact factor: 3.488

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

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Journal:  J Chem Theory Comput       Date:  2012-11-29       Impact factor: 6.006

3.  MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

Authors:  Robert T McGibbon; Kyle A Beauchamp; Matthew P Harrigan; Christoph Klein; Jason M Swails; Carlos X Hernández; Christian R Schwantes; Lee-Ping Wang; Thomas J Lane; Vijay S Pande
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4.  Flexible simple point-charge water model with improved liquid-state properties.

Authors:  Yujie Wu; Harald L Tepper; Gregory A Voth
Journal:  J Chem Phys       Date:  2006-01-14       Impact factor: 3.488

5.  A general purpose model for the condensed phases of water: TIP4P/2005.

Authors:  J L F Abascal; C Vega
Journal:  J Chem Phys       Date:  2005-12-15       Impact factor: 3.488

6.  Statistically optimal analysis of samples from multiple equilibrium states.

Authors:  Michael R Shirts; John D Chodera
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

7.  Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming.

Authors:  Benjamin G Levine; John E Stone; Axel Kohlmeyer
Journal:  J Comput Phys       Date:  2011-05-01       Impact factor: 3.553

8.  OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

Authors:  Peter Eastman; Mark S Friedrichs; John D Chodera; Randall J Radmer; Christopher M Bruns; Joy P Ku; Kyle A Beauchamp; Thomas J Lane; Lee-Ping Wang; Diwakar Shukla; Tony Tye; Mike Houston; Timo Stich; Christoph Klein; Michael R Shirts; Vijay S Pande
Journal:  J Chem Theory Comput       Date:  2012-10-18       Impact factor: 6.006

9.  Building Water Models: A Different Approach.

Authors:  Saeed Izadi; Ramu Anandakrishnan; Alexey V Onufriev
Journal:  J Phys Chem Lett       Date:  2014-10-16       Impact factor: 6.475

10.  Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.

Authors:  David J Huggins
Journal:  J Chem Phys       Date:  2012-02-14       Impact factor: 3.488

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Authors:  Tai-Sung Lee; Bryce K Allen; Timothy J Giese; Zhenyu Guo; Pengfei Li; Charles Lin; T Dwight McGee; David A Pearlman; Brian K Radak; Yujun Tao; Hsu-Chun Tsai; Huafeng Xu; Woody Sherman; Darrin M York
Journal:  J Chem Inf Model       Date:  2020-09-16       Impact factor: 4.956

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Journal:  J Chem Inf Model       Date:  2019-03-22       Impact factor: 4.956

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Journal:  Sci Rep       Date:  2022-02-11       Impact factor: 4.379

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