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Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

✍ Scribed by Peter Eastman; Vijay S. Pande

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
216 KB
Volume
31
Category
Article
ISSN
0192-8651

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✦ Synopsis

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. Β© 2009 Wiley Periodicals, Inc. J Comput Chem, 2010

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