Optimization of Parameters for Molecular Dynamics Simulation Using Smooth Particle-Mesh Ewald in GROMACS 4.5
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...[Show more]
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|Source:||Journal of Computational Chemistry|
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