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Center for Research Computing (CRC)
and Department of Chemical and
Biomolecular Engineering Colloquium
Tuesday, May 1, 2007 at 3:30 p.m.
"Avoiding the Bottleneck in Molecular Dynamics Simulations"
Daniel Gezelter
Department of Chemistry and Biochemistry
University of Notre Dame
Room 131 DeBartolo Hall
Abstract:
Typically, the most computationally demanding portion of a classical molecular dynamics simulation is the calculation of electrostatic interactions between atoms. The standard method (the Ewald sum) is at best an O(N log N) task. In this talk, we'll discuss viable and computationally efficient O(N) alternatives to the Ewald sum for typical modern molecular simulations. These methods are extended from the damped and cutoff-neutralized Coulombic sum originally proposed by Wolf et al. One of these, the damped shifted force method, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques. Comparisons were performed with this and other pairwise methods against the smooth particle mesh Ewald (SPME) summation to see how well they reproduce the energetics and dynamics of a variety of molecular simulations. We extend this technique to handle interactions between electrostatic multipoles. We also investigate the effects of damped and shifted electrostatics on the static, thermodynamic, dynamic and dielectric properties of liquid water and various polymorphs of ice.