The GROMOS96 benchmarks for molecular simulation

Bonvin, Alexandre M. J. J., Mark, Alan E. and van Gunsteren, Wilfred F. (2000) The GROMOS96 benchmarks for molecular simulation. Computer Physics Communications, 128 3: 550-557. doi:10.1016/S0010-4655(99)00540-8

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Author Bonvin, Alexandre M. J. J.
Mark, Alan E.
van Gunsteren, Wilfred F.
Title The GROMOS96 benchmarks for molecular simulation
Journal name Computer Physics Communications   Check publisher's open access policy
ISSN 0010-4655
Publication date 2000-06-01
Sub-type Article (original research)
DOI 10.1016/S0010-4655(99)00540-8
Open Access Status File (Author Post-print)
Volume 128
Issue 3
Start page 550
End page 557
Total pages 8
Place of publication Netherlands
Publisher Elsevier BV * North-Holland
Language eng
Abstract A set of biomolecular systems is presented, which can be used to benchmark the performance of simulation programs and computers. It is applied, using the GROMOS96 biomolecular simulation software, to a variety of computers. The dependence of computing time on a number of model and computational parameters is investigated. An extended pair list technique to select non-bonded interaction pairs and long-range interactions is shown to increase the efficiency by a factor 1.5 to 3 when compared to standard procedures. The benchmark results can be used to estimate the computer time required for simulation studies, and to evaluate the efficiency of various computers regarding molecular simulations.
Keyword Molecular dynamics
Non-bonded interactions
Cut-offs
Extended pair list
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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Citation counts: TR Web of Science Citation Count  Cited 19 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 23 Mar 2011, 22:03:42 EST by Professor Alan Mark on behalf of School of Chemistry & Molecular Biosciences