Accelerating molecular dynamic simulation on the cell processor and Playstation 3.
Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors.
Luttmann
Edgar
E
Department of Chemistry, Stanford University, Stanford, California 94305, USA.
Ensign
Daniel L
DL
Vaidyanathan
Vishal
V
Houston
Mike
M
Rimon
Noam
N
Øland
Jeppe
J
Jayachandran
Guha
G
Friedrichs
Mark
M
Pande
Vijay S
VS
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular