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Software News and Updates Performance Enhancements for GROMACS Nonbonded Interactions on BlueGene

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Abraham, Mark

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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.

dc.contributor.authorAbraham, Mark
dc.date.accessioned2015-12-10T22:15:15Z
dc.identifier.issn0192-8651
dc.identifier.urihttp://hdl.handle.net/1885/50558
dc.description.abstractSeveral 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.
dc.publisherJohn Wiley & Sons Inc
dc.sourceJournal of Computational Chemistry
dc.subjectKeywords: BlueGene; GROMACS; PowerPC; rounding; SIMD optimization; Molecular dynamics; Table lookup; Optimization; article; computer program; molecular dynamics; Molecular Dynamics Simulation; Software BlueGene; GROMACS; PowerPC; rounding; SIMD optimization; table lookups
dc.titleSoftware News and Updates Performance Enhancements for GROMACS Nonbonded Interactions on BlueGene
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume32
dc.date.issued2011
local.identifier.absfor060199 - Biochemistry and Cell Biology not elsewhere classified
local.identifier.ariespublicationu4020362xPUB206
local.type.statusPublished Version
local.contributor.affiliationAbraham, Mark, College of Medicine, Biology and Environment, ANU
local.description.embargo2037-12-31
local.bibliographicCitation.issue9
local.bibliographicCitation.startpage2041
local.bibliographicCitation.lastpage2046
local.identifier.doi10.1002/jcc.21766
dc.date.updated2016-02-24T10:27:18Z
local.identifier.scopusID2-s2.0-79955473704
CollectionsANU Research Publications

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