Parallel programming library for molecular dynamics simulations

R Trobec and M Sterk and M Praprotnik and D Janezic, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 96, 530-536 (2004).

DOI: 10.1002/qua.10742

parallel programming library for molecular dynamics (MD) simulations is described and applied to the recently proposed split integration symplectic method (SISM) for MD simulation. The results show that for a system of 1024 linear chain molecules with an integration step of 4.5 fs. parallel execution of SISM with the particle-particle interactions (PPIs) library on 32 computers gives efficiency of 95.6%. The results also show the parallel simulation of n particles is scalable with the number of processors p and the time requirement is proportional to n(2)/p for n/p large enough, which guarantees optimal speed-up. (C) 2003 Wiley Periodicals, Inc.

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