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Gridifying the TINKER Conformer Generator Application for gLite Grid

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Part of the book series:Lecture Notes in Computer Science ((LNTCS,volume 6586))

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Abstract

Grid Computing provides an efficient way for parallelizing and gridifying computationally and data intensive applications of various research fields. One of these application areas is molecular dynamics. In this paper we examine a biochemical application that generates conformers by unconstrained molecular dynamics at high temperature to overcome conformational bias then finishes each conformer by simulated annealing and energy minimization to obtain reliable structures. We provide a general way for turning biochemical applications into Grid workflows that can be executed by Grid portals exploiting the computational power of available production Grids. First we describe the gridification process, then provide experimental results that show the achieved speed-up of the ported application.

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Author information

Authors and Affiliations

  1. MTA SZTAKI Computer and Automation Research Institute, H-1518, Budapest, P.O. Box 63, Hungary

    Attila Kertész & Péter Kacsuk

  2. Biological Research Center, H-6701, Szeged, P.O. Box 521, Hungary

    Ferenc Ötvös

Authors
  1. Attila Kertész

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  2. Ferenc Ötvös

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  3. Péter Kacsuk

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Editor information

Editors and Affiliations

  1. CNR, ICAR, Via P. Castellino, 111, 80131, Napoli, Italy

    Mario R. Guarracino

  2. INRIA,  PIP ENS Lyon, 46 Allée d’Italie, 69364, Lyon, France

    Frédéric Vivien

  3. Scientific Computing, University of Vienna, Nordbergstr. 15/3C, 1090, Vienna, Austria

    Jesper Larsson Träff

  4. University of Catanzaro, 88100, Catanzaro, Italy

    Mario Cannatoro

  5. Dept. of Computer Science, University of Pisa, Via Tevere 17, 56122, Pisa, Italy

    Marco Danelutto

  6. Gavle Creative Media Lab, Kungsbacksvagen 47, 80632, Gavle, Sweden

    Anders Hast

  7. Dept. Math & Stat, University of Naples Parthenope, via Medina 40, 80133, Napoli, Italy

    Francesca Perla

  8. TU Dresden, Zellescher Weg 12-14, 01187, Dresden, Germany

    Andreas Knüpfer

  9. Dipartimento di Ingegneria dell’ Informazione, Seconda Università di Napoli, via Roma 29, 81031, Aversa, Italy

    Beniamino Di Martino

  10. Scaledinfra technologies GmbH, Köllnerhofgasse 3/15A, 1010, Vienna, Austria

    Michael Alexander

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© 2011 Springer-Verlag Berlin Heidelberg

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Kertész, A., Ötvös, F., Kacsuk, P. (2011). Gridifying the TINKER Conformer Generator Application for gLite Grid. In: Guarracino, M.R.,et al. Euro-Par 2010 Parallel Processing Workshops. Euro-Par 2010. Lecture Notes in Computer Science, vol 6586. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21878-1_23

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