Literature DB >> 25100924

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

Takefumi Yamashita1, Yuxing Peng2, Chris Knight3, Gregory A Voth4.   

Abstract

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.

Entities:  

Keywords:  coarse-graining; effective long-range interaction; multiple-program parallelization; reactive molecular dynamics

Year:  2012        PMID: 25100924      PMCID: PMC4120847          DOI: 10.1021/ct3006437

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


  43 in total

1.  Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane.

Authors:  Alexander M Smondyrev; Gregory A Voth
Journal:  Biophys J       Date:  2002-03       Impact factor: 4.033

2.  Computer simulation of sedimentation of ionic systems using the Wolf method.

Authors:  P X Viveros-Méndez; Alejandro Gil-Villegas
Journal:  J Chem Phys       Date:  2012-04-21       Impact factor: 3.488

3.  Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics.

Authors:  Christopher J Fennell; J Daniel Gezelter
Journal:  J Chem Phys       Date:  2006-06-21       Impact factor: 3.488

4.  Coarse-graining in interaction space: an analytical approximation for the effective short-ranged electrostatics.

Authors:  Qiang Shi; Pu Liu; Gregory A Voth
Journal:  J Phys Chem B       Date:  2008-12-18       Impact factor: 2.991

5.  Hydrated excess proton at water-hydrophobic interfaces.

Authors:  Satoru Iuchi; Hanning Chen; Francesco Paesani; Gregory A Voth
Journal:  J Phys Chem B       Date:  2009-04-02       Impact factor: 2.991

6.  A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions.

Authors:  Ivan S Ufimtsev; Andrey G Kalinichev; Todd J Martinez; R James Kirkpatrick
Journal:  Phys Chem Chem Phys       Date:  2009-08-27       Impact factor: 3.676

7.  Insights into the mechanism of proton transport in cytochrome c oxidase.

Authors:  Takefumi Yamashita; Gregory A Voth
Journal:  J Am Chem Soc       Date:  2012-01-06       Impact factor: 15.419

8.  Properties of hydrated excess protons near phospholipid bilayers.

Authors:  Takefumi Yamashita; Gregory A Voth
Journal:  J Phys Chem B       Date:  2010-01-14       Impact factor: 2.991

Review 9.  Computer simulation of proton solvation and transport in aqueous and biomolecular systems.

Authors:  Gregory A Voth
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

10.  Proton transport behavior through the influenza A M2 channel: insights from molecular simulation.

Authors:  Hanning Chen; Yujie Wu; Gregory A Voth
Journal:  Biophys J       Date:  2007-08-10       Impact factor: 4.033

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  23 in total

1.  Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase.

Authors:  Ruibin Liang; Jessica M J Swanson; Mårten Wikström; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-23       Impact factor: 11.205

2.  Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale.

Authors:  Chenghan Li; Zhi Yue; L Michel Espinoza-Fonseca; Gregory A Voth
Journal:  Biophys J       Date:  2020-08-06       Impact factor: 4.033

3.  A Computational Swiss Army Knife Approach to Unraveling the Secrets of Proton Movement through SERCA.

Authors:  Syma Khalid; Simon Newstead
Journal:  Biophys J       Date:  2020-08-06       Impact factor: 4.033

4.  Acid activation mechanism of the influenza A M2 proton channel.

Authors:  Ruibin Liang; Jessica M J Swanson; Jesper J Madsen; Mei Hong; William F DeGrado; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-24       Impact factor: 11.205

5.  Local conformational dynamics regulating transport properties of a Cl- /H+ antiporter.

Authors:  Zhi Wang; Jessica M J Swanson; Gregory A Voth
Journal:  J Comput Chem       Date:  2019-10-21       Impact factor: 3.376

6.  Classical Molecular Dynamics with Mobile Protons.

Authors:  Themis Lazaridis; Gerhard Hummer
Journal:  J Chem Inf Model       Date:  2017-11-14       Impact factor: 4.956

7.  Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase.

Authors:  Ruibin Liang; Jessica M J Swanson; Yuxing Peng; Mårten Wikström; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-23       Impact factor: 11.205

8.  Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter.

Authors:  Sangyun Lee; Jessica M J Swanson; Gregory A Voth
Journal:  Biophys J       Date:  2016-03-29       Impact factor: 4.033

9.  Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.

Authors:  Chenghan Li; Jessica M J Swanson
Journal:  J Phys Chem B       Date:  2020-06-24       Impact factor: 2.991

10.  Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel.

Authors:  Ruibin Liang; Hui Li; Jessica M J Swanson; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-16       Impact factor: 11.205

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