A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics
Department of Chemical and Biological Engineering, Northwestern University, Evanston Illinois 60201
Journal of Chemical Theory and Computation, Vol. 6, No. 10. (12 October 2010), pp. 3058-3065
@article{jhagraphics,
title={A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics},
author={Jha, P.K. and Sknepnek, R. and Guerrero-Garcia, G.I. and Olvera de la Cruz, M.},
journal={Journal of Chemical Theory and Computation},
pages={5342–5359},
issn={1549-9618},
publisher={ACS Publications}
}
We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of electrolytes. Our GPU implementation is significantly faster than the CPU implementation of the Ewald method for small to a sizable number of particles (~10^5). Thermodynamic and structural properties of monovalent and divalent hydrated salts in the bulk are calculated for a wide range of ionic concentrations. An excellent agreement between the two methods was found at the level of electrostatic energy, heat capacity, radial distribution functions, and integrated charge of the electrolytes.
January 25, 2011 by hgpu
