title: Accelerating molecular dynamic simulation on the cell processor and Playstation 3.
abstract: 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.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors.forename: Edgar
authors.initials: E
authors.lastname: Luttmann
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Ensign
authors.forename: Vishal
authors.initials: V
authors.lastname: Vaidyanathan
authors.forename: Mike
authors.initials: M
authors.lastname: Houston
authors.forename: Noam
authors.initials: N
authors.lastname: Rimon
authors.forename: Jeppe
authors.initials: J
authors.lastname: Øland
authors.forename: Guha
authors.initials: G
authors.lastname: Jayachandran
authors.forename: Mark
authors.initials: M
authors.lastname: Friedrichs
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular