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

Journal Article · Mon Jan 01 00:00:00 EST 2007 · Theoretical Chemistry Accounts, 117(1):73-84

OSTI ID:899150

Fanourgakis, Georgios S; Tipparaju, Vinod; Nieplocha, Jarek; Xantheas, Sotiris S

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.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 899150
• Report Number(s): PNNL-SA-46786; 3565; KC0301020; TRN: US200706%%387
• Journal Information: Theoretical Chemistry Accounts, 117(1):73-84, Journal Name: Theoretical Chemistry Accounts, 117(1):73-84
• Country of Publication: United States
• Language: English

Related Subjects

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