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Optimization of parameters for molecular dynamics simulation using smooth particle‐mesh Ewald in GROMACS 4.5
Author(s) -
Abraham Mark J.,
Gready Jill E.
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21773
Subject(s) - molecular dynamics , computer science , range (aeronautics) , computational science , electrostatics , ewald summation , work (physics) , reliability (semiconductor) , parameter space , computation , space (punctuation) , particle (ecology) , algorithm , computational chemistry , physics , chemistry , mathematics , materials science , quantum mechanics , power (physics) , oceanography , geology , composite material , operating system , statistics
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