Gridifying the TINKER conformer generator application for gLite grid

Attila Kertész, Ferenc Ötvös, Péter Kacsuk

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

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.

Original languageEnglish
Title of host publicationEuro-Par 2010 - Parallel Processing Workshops
Subtitle of host publicationHeteroPar, HPPC, HiBB, CoreGrid, UCHPC, HPCF, PROPER, CCPI, VHPC, Revised Selected Papers
Pages185-192
Number of pages8
DOIs
Publication statusPublished - Aug 19 2011
EventParallel Processing Workshops, Euro-Par 2010: HeteroPar 2010, HPPC 2010, HiBB 2010, CoreGrid 2010, UCHPC 2010, HPCF 2010, PROPER 2010, CCPI 2010, VHPC 2010 - Ischia, Italy
Duration: Aug 31 2010Sep 3 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6586 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherParallel Processing Workshops, Euro-Par 2010: HeteroPar 2010, HPPC 2010, HiBB 2010, CoreGrid 2010, UCHPC 2010, HPCF 2010, PROPER 2010, CCPI 2010, VHPC 2010
CountryItaly
CityIschia
Period8/31/109/3/10

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Keywords

  • Grid Computing
  • Grid portal
  • TINKER application.
  • molecule conformer generation

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Kertész, A., Ötvös, F., & Kacsuk, P. (2011). Gridifying the TINKER conformer generator application for gLite grid. In Euro-Par 2010 - Parallel Processing Workshops: HeteroPar, HPPC, HiBB, CoreGrid, UCHPC, HPCF, PROPER, CCPI, VHPC, Revised Selected Papers (pp. 185-192). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6586 LNCS). https://doi.org/10.1007/978-3-642-21878-1_23