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Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

P. Eastman, V. S. Pande
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}

}

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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.
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