The GROMOS96 benchmarks for molecular simulation

AMJJ Bonvin; AE Mark; WF van Gunsteren

doi:10.1016/S0010-4655(99)00540-8

The GROMOS96 benchmarks for molecular simulation

AMJJ Bonvin, AE Mark, WF van Gunsteren

Research output: Contribution to journal › Article › Academic › peer-review

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. (C) 2000 Elsevier Science B.V. All rights reserved.

Original language	English
Pages (from-to)	550-557
Number of pages	8
Journal	Computer Physics Communications
Volume	128
Issue number	3
DOIs	https://doi.org/10.1016/S0010-4655(99)00540-8
Publication status	Published - Jun 2000

Keywords

Cut-offs
Extended pair list
Molecular dynamics
Non-bonded interactions

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10.1016/S0010-4655(99)00540-8

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title = "The GROMOS96 benchmarks for molecular simulation",

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. (C) 2000 Elsevier Science B.V. All rights reserved.",

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AU - van Gunsteren, WF

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N2 - 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. (C) 2000 Elsevier Science B.V. All rights reserved.

AB - 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. (C) 2000 Elsevier Science B.V. All rights reserved.

KW - Cut-offs

KW - Extended pair list

KW - Molecular dynamics

KW - Non-bonded interactions

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JO - Computer Physics Communications

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The GROMOS96 benchmarks for molecular simulation

Abstract

Keywords

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