Literature DB >> 28845049

Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization.

Christopher Arntsen1, Chen Chen1,2, Gregory A Voth1.   

Abstract

We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.

Entities:  

Keywords:  Reactive molecular dynamics; acids; hydrated excess proton; multiscale modeling; relative entropy minimization

Year:  2017        PMID: 28845049      PMCID: PMC5568817          DOI: 10.1016/j.cplett.2017.04.064

Source DB:  PubMed          Journal:  Chem Phys Lett        ISSN: 0009-2614            Impact factor:   2.328


  18 in total

1.  Relative entropy as a universal metric for multiscale errors.

Authors:  Aviel Chaimovich; M Scott Shell
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-06-29

Review 2.  Chance and design--proton transfer in water, channels and bioenergetic proteins.

Authors:  Colin A Wraight
Journal:  Biochim Biophys Acta       Date:  2006-07-14

3.  The relative entropy is fundamental to multiscale and inverse thermodynamic problems.

Authors:  M Scott Shell
Journal:  J Chem Phys       Date:  2008-10-14       Impact factor: 3.488

4.  Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy.

Authors:  Aviel Chaimovich; M Scott Shell
Journal:  Phys Chem Chem Phys       Date:  2009-01-27       Impact factor: 3.676

5.  Coarse-graining errors and numerical optimization using a relative entropy framework.

Authors:  Aviel Chaimovich; M Scott Shell
Journal:  J Chem Phys       Date:  2011-03-07       Impact factor: 3.488

6.  An analysis of hydrated proton diffusion in ab initio molecular dynamics.

Authors:  Ying-Lung Steve Tse; Chris Knight; Gregory A Voth
Journal:  J Chem Phys       Date:  2015-01-07       Impact factor: 3.488

7.  Perspective: How good is DFT for water?

Authors:  Michael J Gillan; Dario Alfè; Angelos Michaelides
Journal:  J Chem Phys       Date:  2016-04-07       Impact factor: 3.488

8.  Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport.

Authors:  Rajib Biswas; Ying-Lung Steve Tse; Andrei Tokmakoff; Gregory A Voth
Journal:  J Phys Chem B       Date:  2015-12-01       Impact factor: 2.991

9.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Gregory A Voth
Journal:  J Phys Chem B       Date:  2007-03-30       Impact factor: 2.991

10.  Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins.

Authors:  Sangyun Lee; Ruibin Liang; Gregory A Voth; Jessica M J Swanson
Journal:  J Chem Theory Comput       Date:  2016-01-20       Impact factor: 6.006

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  1 in total

1.  Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data.

Authors:  Chen Chen; Christopher Arntsen; Gregory A Voth
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

  1 in total

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