Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L

M. Sekijima, J. Doi, T. Noguchi, Y. Akiyama, and S. Shimizu (Japan)


molecular dynamics (MD) simulation, high performance computing, code optimization, scientific computing


We introduce a parallelized molecular dynamics (MD) simulation adapted for the IBM Blue Gene/L supercomputer. We begin by describing the Parallel MD code. Next we discuss how Parallel MD was tuned for Blue Gene/L. We then show the results for some test targets, related to disease associated proteins, that we have run on Blue Gene/L and the efficiency we have achieved. Finally, we mention some future directions that we envisage undertaking as a continuation of this project.

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