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Accelerating molecular dynamic simulation on the cell processor and Playstation 3
Author(s) -
Luttmann Edgar,
Ensign Daniel L.,
Vaidyanathan Vishal,
Houston Mike,
Rimon Noam,
Øland Jeppe,
Jayachandran Guha,
Friedrichs Mark,
Pande Vijay S.
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21054
Subject(s) - computer science , parallel computing , computation , molecular dynamics , coprocessor , power (physics) , computational science , solvation , computer architecture , chemistry , physics , computational chemistry , ion , organic chemistry , algorithm , quantum mechanics
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. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009