A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions

Authors

  • David E. Shaw

    Corresponding author
    1. D. E. Shaw Research and Development, LLC and Center for Computational Biology and Bioinformatics, Columbia University, 120 W. 45th St., 39th floor, New York, New York 10036
    • D. E. Shaw Research and Development, LLC and Center for Computational Biology and Bioinformatics, Columbia University, 120 W. 45th St., 39th floor, New York, New York 10036
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Abstract

Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R3/2p−1/2), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1318–1328, 2005

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