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Parallel biomolecular simulation: An overview and analysis of important algorithms

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High-Performance Computing and Networking (HPCN-Europe 1996)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1067))

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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.

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Authors and Affiliations

  1. Institute for Theoretical Chemistry, Theoretical Biochemistry Group, University of Vienna, Währingerstraße 17/Parterre, A-1090, Wien, Austria

    Gerald Löffler & Hellfried Schreiber

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  1. Gerald Löffler
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  2. Hellfried Schreiber
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Heather Liddell Adrian Colbrook Bob Hertzberger Peter Sloot

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© 1996 Springer-Verlag Berlin Heidelberg

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Löffler, G., Schreiber, H. (1996). Parallel biomolecular simulation: An overview and analysis of important algorithms. In: Liddell, H., Colbrook, A., Hertzberger, B., Sloot, P. (eds) High-Performance Computing and Networking. HPCN-Europe 1996. Lecture Notes in Computer Science, vol 1067. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-61142-8_653

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  • DOI: https://doi.org/10.1007/3-540-61142-8_653

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-61142-4

  • Online ISBN: 978-3-540-49955-8

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