A Monte Carlo approach for processor allocation in molecular dynamics simulations

A Monte Carlo algorithm for optimal processor allocation for Molecular Dynamics simulations of proteins on Single Instruction Multiple Data flow computer is presented. The algorithm starts from a conventional data structure based on space decomposition algorithm and produces a modified structure based on the atom decomposition approach, optimised in term of computation and communication time. The authors' approach is well suited for Molecular Dynamics simulations on massively parallel computers based on square or cubic communication networks.<
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