Parallel algorithms for molecular dynamics with induction forces

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.

• Type: Journal
• Year: 2008
• Where: CPHYSICS
• Authors: Jianhui Li, Zhongwu Zhou, Richard J. Sadus
• Keywords: CPHYSICS 2008, Induction Interactions, Long-range Induction Interactions, Molecular Dynamics Simulations