Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
Department of Bioengineering, Stanford University, Stanford, CA 94305
J. Comput. Chem., Vol. 31, No. 6. (21 October 2010), pp. 1268-1272.
@article{eastman2010efficient,
title={Efficient nonbonded interactions for molecular dynamics on a graphics processing unit},
author={Eastman, P. and Pande, V.S.},
journal={Journal of Computational Chemistry},
volume={31},
number={6},
pages={1268–1272},
issn={1096-987X},
year={2010},
publisher={Wiley Online Library}
}
We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high-performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms.
November 7, 2010 by hgpu
