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Title: An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water

Abstract

An efficient parallelization scheme for classical Molecular Dynamics simulations with flexible polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during Molecular Dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128-512 water molecules employing two exible, polarizable water models [POL1(F) and TTM2-F] containing 1 and 3 polarizable sites respectively. The efficiency of the algorithm, is evaluated against a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculations of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed in several cases. To the best of our knowledge, this is the first attempt for a parallel implementation of a polarizable potential under periodic boundary conditions. Guidelines for adapting the algorithm for larger systems are also discussed. This research was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences laboratory,more » a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research located at the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
899150
Report Number(s):
PNNL-SA-46786
3565; KC0301020; TRN: US200706%%387
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Theoretical Chemistry Accounts, 117(1):73-84
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; 37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; WATER; MOLECULAR DYNAMICS METHOD; PARALLEL PROCESSING; POLARIZATION; MANY-BODY PROBLEM; ALGORITHMS; DIPOLE MOMENTS; ELECTROSTATICS; PERFORMANCE; Molecular Dynamics; flexible polarizable empirical potentials; Ewald summation technique; electrostastic interactions; induction interactions; Environmental Molecular Sciences Laboratory

Citation Formats

Fanourgakis, Georgios S., Tipparaju, Vinod, Nieplocha, Jarek, and Xantheas, Sotiris S.. An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water. United States: N. p., 2007. Web.
Fanourgakis, Georgios S., Tipparaju, Vinod, Nieplocha, Jarek, & Xantheas, Sotiris S.. An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water. United States.
Fanourgakis, Georgios S., Tipparaju, Vinod, Nieplocha, Jarek, and Xantheas, Sotiris S.. Mon . "An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water". United States. doi:.
@article{osti_899150,
title = {An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: Application to water},
author = {Fanourgakis, Georgios S. and Tipparaju, Vinod and Nieplocha, Jarek and Xantheas, Sotiris S.},
abstractNote = {An efficient parallelization scheme for classical Molecular Dynamics simulations with flexible polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during Molecular Dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128-512 water molecules employing two exible, polarizable water models [POL1(F) and TTM2-F] containing 1 and 3 polarizable sites respectively. The efficiency of the algorithm, is evaluated against a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculations of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed in several cases. To the best of our knowledge, this is the first attempt for a parallel implementation of a polarizable potential under periodic boundary conditions. Guidelines for adapting the algorithm for larger systems are also discussed. This research was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences laboratory, a national scientific user facility sponsored by the U.S. Department of Energy’s Office of Biological and Environmental Research located at the Pacific Northwest National Laboratory. The Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy under contract DE-AC05-76RL01830.},
doi = {},
journal = {Theoretical Chemistry Accounts, 117(1):73-84},
number = ,
volume = ,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}