A domain decomposition parallelization strategy for molecular dynamics simulations on distributed memory machines

Abstract An algorithm is described which allows large scale molecular dynamics simulations to be carried out on a distributed memory parallel computer. The method is a development of a spatial decomposition technique already described [S.Y. Liem, D. Brown and J.H.R. Clarke, Comput. Phys. Commun. 67 (1991) 261] but incorporates decomposition of 3-D space in all three dimensions with link-cell and neighbour table techniques for enhanced efficiency. It is shown that communications between processors can be minimized without incurring the penalties associated with redundant force calculations. The method has been tested on a Fujitsu AP1000 parallel machine with up to 512 processor elements.

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