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).
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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