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J Comput Chem. 2010 Apr 30;31(6):1268-72. doi: 10.1002/jcc.21413.

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit.

Author information

1
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. peastman@stanford.edu

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.

PMID:
19847780
PMCID:
PMC2841709
DOI:
10.1002/jcc.21413
[Indexed for MEDLINE]
Free PMC Article

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