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

  • Piotr Bała
  • Paweł Grochowski
  • Krzysztof Nowiński
  • Terry Clark
  • Bogdan Lesyng
  • James Andrew McCammon
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1541)

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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Copyright information

© Springer-Verlag Berlin Heidelberg 1998

Authors and Affiliations

  • Piotr Bała
    • 1
    • 2
  • Paweł Grochowski
    • 1
  • Krzysztof Nowiński
    • 1
  • Terry Clark
    • 3
  • Bogdan Lesyng
    • 1
  • James Andrew McCammon
    • 4
    • 5
  1. 1.Interdisciplinary Centre for Mathematical and Computational ModellingWarsaw UniversityWarsawPoland
  2. 2.Institute of PhysicsN. Copernicus UniversityToruńPoland
  3. 3.Baylor College of Medicine and Texas Center for Advanced Molecular ComputationHoustonUSA
  4. 4.Department of Chemistry and BiochemistryUniversity of California at San DiegoLa JollaUSA
  5. 5.Department of PharmacologyUniversity of California at San DiegoLa JollaUSA

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