Efficient nonbonded interactions for molecular dynamics on a graphics processing unit |
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Authors: | Peter Eastman Vijay S Pande |
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Institution: | 1. Department of Bioengineering, Stanford University, Stanford, CA 94305;2. Department of Chemistry, Stanford University, Stanford, CA 94305 |
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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, 2010 |
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Keywords: | molecular dynamics graphics processing unit GPU nonbonded cutoff reaction field explicit solvent water |
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