Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
- 21 October 2009
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 31 (6) , 1268-1272
- https://doi.org/10.1002/jcc.21413
Abstract
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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010Keywords
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