Kertesz, Attila and Otvos, Ferenc and Kacsuk, Peter K. (2011) Gridifying the TINKER conformer generator application for gLite grid. In: Guarracino, Mario R. and Vivien, Frederic and Larsson Traff, Jesper and Cannataro, Mario and Danelutto, Marco and Hast, Anders and Perla, Francesca and Knupfer, Andreas and Di Martino, Beniamino and Alexander, Michael, (eds.) Euro-Par 2010 parallel processing workshops. Lecture notes in computer science (6586). Springer, pp. 185-192. ISBN 9783642218774
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Official URL: http://dx.doi.org/ 10.1007/978-3-642-21878-1_23
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.
| Item Type: | Book Section |
|---|---|
| Research Community: | University of Westminster > Electronics and Computer Science, School of |
| ID Code: | 11057 |
| Deposited On: | 07 Aug 2012 09:42 |
| Last Modified: | 07 Aug 2012 09:42 |
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