Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 30, Issue 6, Pages 864-872Publisher
WILEY
DOI: 10.1002/jcc.21209
Keywords
GPU; molecular dynamics; implicit solvent
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We describe it complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU). including all standard force field terms, integration. constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance. and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. (C) 2009 Wiley Periodicals, Inc. J Comput Client 30: 864-872, 2009
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