Accelerating molecular dynamic simulation on graphics processing units.
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.
Friedrichs
Mark S
MS
Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
Eastman
Peter
P
Vaidyanathan
Vishal
V
Houston
Mike
M
Legrand
Scott
S
Beberg
Adam L
AL
Ensign
Daniel L
DL
Bruns
Christopher M
CM
Pande
Vijay S
VS
D000465:Algorithms; D019295:Computational Biology / Q000191:economics / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation / Q000191:economics*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013997:Time Factors
D011506:Proteins; D012997:Solvents