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Accelerating molecular dynamic simulation on graphics processing units

✍ Scribed by Mark S. Friedrichs; Peter Eastman; Vishal Vaidyanathan; Mike Houston; Scott Legrand; Adam L. Beberg; Daniel L. Ensign; Christopher M. Bruns; Vijay S. Pande

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
624 KB
Volume
30
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

We describe a 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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009

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