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Parallel biomolecular simulation: An overview and analysis of important algorithms

  • Gerald Löffler
  • Hellfried Schreiber
Posters
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1067)

Abstract

We have presented important algorithms for serial MD simulations of biomedical systems and have analysed their impact on parallel performance. None of these algorithms can be neglected if we are interested in true gains in throughput and not just in good formal scalability numbers. This is especially true for the SHAKE algorithm, which due to its small contribution to the total runtime and due to its inherently serial character is often not included in reports on the parallelisation of MD programs. We have shown clearly that even a very modest speedup in this algorithm is essential for increased overall performance.

Keywords

Water Molecule Molecular Dynamics Molecular Dynamics Simulation Total Runtime Force Calculation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 1996

Authors and Affiliations

  • Gerald Löffler
    • 1
  • Hellfried Schreiber
    • 1
  1. 1.Institute for Theoretical Chemistry, Theoretical Biochemistry GroupUniversity of ViennaWienAustria

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