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Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5
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]

Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.

Place, publisher, year, edition, pages
John Wiley & Sons, 2011. Vol. 32, no 9
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-182273DOI: 10.1002/jcc.21773ISI: 000290531000026PubMedID: 21469158Scopus ID: 2-s2.0-79955479719OAI: oai:DiVA.org:kth-182273DiVA: diva2:904183
Note

QC 20160226

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

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