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Parallel Molecular Dynamics Using Force Decomposition

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Computational Molecular Dynamics: Challenges, Methods, Ideas

Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 4))

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Abstract

Research interests in molecular dynamics (MD) and its applications have increased significantly over the past few decades. This is due partly to the advances in software and hardware components of computer technology. The main computational goal of recent research work in molecular dynamics has been to reduce the computational cost of the force calculations which evidently accounts for approximately ninety percent of the total CPU time for most MD simulations. This paper describes parallel algorithms for force calculations using the force decomposition approach. These parallel algorithms have been tested and found to be highly portable and scalable. Numerical experiments on IBM SP/2 indicate that these algorithms have improved speedups and efficiencies.

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Authors and Affiliations

  1. Department of Computer Science, University of Missouri-Rolla, Rolla, MO, 65401, USA

    Daniel Okunbor & Ravi Murty

Authors
  1. Daniel Okunbor
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  2. Ravi Murty
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Editor information

Editors and Affiliations

  1. Konrad-Zuse-Zentrum Berlin (ZIB), Takustrasse 7, D-14195, Berlin-Dahlem, Germany

    Peter Deuflhard

  2. Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599-7260, USA

    Jan Hermans

  3. Department of Mathematics, University of Kansas, 405 Snow Hall, Lawrence, KS, 66045, USA

    Benedict Leimkuhler

  4. Laboratorium für Physikalische Chemie ETH Zentrum, CH-8092, Zürich, Switzerland

    Alan E. Mark

  5. Department of Mathematics and Statistics, University of Surrey, Guildford, Surrey, GU2 5XH, UK

    Sebastian Reich

  6. Department of Computer Science, University of Illinois, 1304 West Springfield Avenue, Urbana, IL, 61801-6631, USA

    Robert D. Skeel

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© 1999 Springer-Verlag Berlin Heidelberg

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Okunbor, D., Murty, R. (1999). Parallel Molecular Dynamics Using Force Decomposition. In: Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A.E., Reich, S., Skeel, R.D. (eds) Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-58360-5_29

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  • DOI: https://doi.org/10.1007/978-3-642-58360-5_29

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63242-9

  • Online ISBN: 978-3-642-58360-5

  • eBook Packages: Springer Book Archive

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