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Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit
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DOI：10.1002/jcc.21413.png)
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Abstract
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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. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 31: 1268-1272, 2010
Keywords:
molecular dynamics
graphics processing unit
GPU
nonbonded
cutoff
reaction field
explicit solvent
water
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