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Advanced calculations and visualization of enzymatic reactions with the combined quantum classical molecular dynamics code

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Book cover Applied Parallel Computing Large Scale Scientific and Industrial Problems (PARA 1998)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1541))

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Abstract

The parallel version of the Quantum Classical Molecular Dynamics code is presented. The execution time scales almost linearly with the number of processors. The measured overhead of the parallelization paradigm is extremely small which ensures the high efficiency of the presented method. Tools based on the Advanced Visualization System (AVS) framework were developed for visualization and analysis of the QCMD simulations.

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Authors and Affiliations

  1. Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawińskiego 5a, 02-106, Warsaw, Poland

    Piotr Bała, Paweł Grochowski, Krzysztof Nowiński & Bogdan Lesyng

  2. Institute of Physics, N. Copernicus University, Grudziądzka 5/7, 87-100, Toruń, Poland

    Piotr Bała

  3. Baylor College of Medicine and Texas Center for Advanced Molecular Computation, Houston, TX, USA

    Terry Clark

  4. Department of Chemistry and Biochemistry, University of California at San Diego, 92093-0365, La Jolla, CA, USA

    James Andrew McCammon

  5. Department of Pharmacology, University of California at San Diego, 92093-0365, La Jolla, CA, USA

    James Andrew McCammon

Authors
  1. Piotr Bała
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  2. Paweł Grochowski
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  3. Krzysztof Nowiński
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  4. Terry Clark
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  5. Bogdan Lesyng
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  6. James Andrew McCammon
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Editor information

Bo Kågström Jack Dongarra Erik Elmroth Jerzy Waśniewski

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© 1998 Springer-Verlag Berlin Heidelberg

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Bała, P., Grochowski, P., Nowiński, K., Clark, T., Lesyng, B., McCammon, J.A. (1998). Advanced calculations and visualization of enzymatic reactions with the combined quantum classical molecular dynamics code. In: Kågström, B., Dongarra, J., Elmroth, E., Waśniewski, J. (eds) Applied Parallel Computing Large Scale Scientific and Industrial Problems. PARA 1998. Lecture Notes in Computer Science, vol 1541. Springer, Berlin, Heidelberg . https://doi.org/10.1007/BFb0095314

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  • DOI: https://doi.org/10.1007/BFb0095314

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-65414-8

  • Online ISBN: 978-3-540-49261-0

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