Parallel algorithms for molecular dynamics with induction forces
JH Li and ZW Zhou and RJ Sadus, COMPUTER PHYSICS COMMUNICATIONS, 178, 384-392 (2008).
We examine parallel algorithms for molecular dynamics simulations involving long-range induction interactions. The algorithms are tested by performing molecular dynamics simulations of water with an intermolecular potential that explicitly includes contributions from pair, three-body and induction interactions. Both cyclic and balanced force decomposition methods are implemented to decompose the parallelizable components of induction, pair and three-body interactions using a message passing interface. We report that more than 90% of the induction calculation, and 98% of the total calculation can be effectively parallelized. A reasonably good speedup of 15.7 times and an efficiency of 49.1% are obtained on 32 processors with the balance force decomposition algorithm. (C) 2007 Elsevier B.V. All rights reserved.
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