2011/04/05 by Mark J. Abraham, M Abraham, Jill E. Gready · 1 citation
Agricultural and Biological Sciences · Materials Science · Biochemistry, Genetics and Molecular Biology · #Plant nutrient uptake and metabolism #Enzyme Structure and Function #Protein Structure and Dynamics
paper · pdf · doi:10.1002/jcc.21773
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.