Gridifying the TINKER conformer generator application for gLite grid

Attila Kertész, F. Ötvös, P. 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 publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages185-192
Number of pages8
Volume6586 LNCS
DOIs
Publication statusPublished - 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)03029743
ISSN (Electronic)16113349

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

Fingerprint

Generator
Grid
Molecular Dynamics
Molecular dynamics
Grid Portal
Grid Workflow
Energy Minimization
Grid computing
Grid Computing
Simulated annealing
Simulated Annealing
Speedup
Experimental Results
Temperature

Keywords

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

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Kertész, A., Ötvös, F., & Kacsuk, P. (2011). Gridifying the TINKER conformer generator application for gLite grid. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6586 LNCS, 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

Gridifying the TINKER conformer generator application for gLite grid. / Kertész, Attila; Ötvös, F.; Kacsuk, P.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6586 LNCS 2011. p. 185-192 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6586 LNCS).

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

Kertész, A, Ötvös, F & Kacsuk, P 2011, Gridifying the TINKER conformer generator application for gLite grid. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 6586 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6586 LNCS, pp. 185-192, Parallel 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, 8/31/10. https://doi.org/10.1007/978-3-642-21878-1_23
Kertész A, Ötvös F, Kacsuk P. Gridifying the TINKER conformer generator application for gLite grid. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6586 LNCS. 2011. p. 185-192. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-642-21878-1_23
Kertész, Attila ; Ötvös, F. ; Kacsuk, P. / Gridifying the TINKER conformer generator application for gLite grid. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6586 LNCS 2011. pp. 185-192 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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