An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water
Fanourgakis, GS (Fanourgakis, George S.); Tipparaju, V (Tipparaju, Vinod); Nieplocha, J (Nieplocha, Jarek); Xantheas, SS (Xantheas, Sotiris S.)
THEORETICAL CHEMISTRY ACCOUNTS, 117 (1): 73-84 JAN 2007
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 to 5 12 molecules employing two flexible, polarizable water models DC(F) and TTM2.1-F containing I and 3 polarizable sites, respectively. The time-to-solution for these two polarizable models is compared with the one for a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient claculation of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed. To the best of our knowledge, this is the first reported results of parallel scaling and performance for simulations of liquid water with a polarizable potential under periodic boundary conditions.
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