OPTIMIZATION AND EVALUATION OF PARALLEL MOLECULAR DYNAMICS SIMULATION ON BLUE GENE/L

摘要

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.