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Performance enhancements for GROMACS nonbonded interactions on BlueGene.
Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, Australia.ORCID iD: 0000-0001-6363-2521
2011 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9Article in journal (Refereed) Published
Abstract [en]

Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.

Place, publisher, year, edition, pages
John Wiley & Sons, 2011. Vol. 32, no 9
National Category
Theoretical Chemistry
URN: urn:nbn:se:kth:diva-182274DOI: 10.1002/jcc.21766ISI: 000290531000027PubMedID: 21469156ScopusID: 2-s2.0-79955473704OAI: diva2:904182

QC 20160226

Available from: 2016-02-18 Created: 2016-02-18 Last updated: 2016-02-26Bibliographically approved

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Abraham, Mark J
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