Accelerating molecular dynamic simulation on graphics processing units
Mark S. Friedrichs(Stanford University), Peter Eastman(Stanford University), Vishal Vaidyanathan(Stanford University), Mike Houston(Advanced Micro Devices (United States)), Scott LeGrand(Nvidia (United States)), Adam L. Beberg(Stanford University), Daniel L. Ensign(Stanford University), Christopher M. Bruns(Stanford University), Vijay S. Pande(Stanford University)
Cited by 550Open Access
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.
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