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

Authors

  • Mark J. Abraham,

    1. Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, ACT, 2601, Australia
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  • Jill E. Gready

    Corresponding author
    1. Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, ACT, 2601, Australia
    • Computational Proteomics Group, John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, ACT, 2601, Australia
    Search for more papers by this author

Abstract

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. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011

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