Parallel algorithms for molecular dynamics with induction forces

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Please use this identifier to cite or link to this item: http://hdl.handle.net/1959.3/30168

Title: Parallel algorithms for molecular dynamics with induction forces
Author(s): Li, Jianhui; Zhou, Zhongwu; Sadus, Richard J.
Abstract: 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.
Publication type: Journal article
Research centre: Swinburne University of Technology. Faculty of Information and Communication Technologies. Centre for Molecular Simulation
Source: Computer Physics Communications, Vol. 178, no. 5 (2008), p. 384-392
Publication year: 2008
Keyword(s): Induction; Molecular dynamics; Parallel algorithms; Water
Publisher: Elsevier
ISSN: 0010-4655
Publisher URL: http://dx.doi.org/10.1016/j.cpc.2007.09.012
Peer reviewed