Accelerating molecular dynamic simulation on the cell processor and Playstation 3 Export

@article{citeulike:3000708, 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. {\copyright} 2008 Wiley Periodicals, Inc. J Comput Chem, 2009}, address = {Department of Chemistry, Stanford University, Stanford, California 94305; Department of Computer Science, Stanford University, Stanford, California 94305; Sony Computer Entertainment America, Redwood City, California}, author = {Luttmann, Edgar and Ensign, Daniel L. and Vaidyanathan, Vishal and Houston, Mike and Rimon, Noam and {\O}land, Jeppe and Jayachandran, Guha and Friedrichs, Mark and Pande, Vijay S.}, citeulike-article-id = {3000708}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.21054}, citeulike-linkout-1 = {http://www3.interscience.wiley.com/cgi-bin/abstract/120736866/ABSTRACT}, citeulike-linkout-2 = {http://www-micrel.deis.unibo.it/~benini/files/MD/StanfordCELL08.pdf}, doi = {10.1002/jcc.21054}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {chemistry, distributed, parallel, ps3, simulation}, number = {2}, pages = {268--274}, posted-at = {2009-10-30 23:06:59}, priority = {2}, title = {Accelerating molecular dynamic simulation on the cell processor and Playstation 3}, url = {http://dx.doi.org/10.1002/jcc.21054}, volume = {30}, year = {2009} }

TY - JOUR ID - citeulike:3000708 L3 - citeulike-article-id:3000708 N2 - 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 IS - 2 JF - Journal of Computational Chemistry SN - 1096-987X AD - Department of Chemistry, Stanford University, Stanford, California 94305; Department of Computer Science, Stanford University, Stanford, California 94305; Sony Computer Entertainment America, Redwood City, California EP - 274 TI - Accelerating molecular dynamic simulation on the cell processor and Playstation 3 VL - 30 SP - 268 KW - chemistry KW - distributed KW - parallel KW - ps3 KW - simulation AU - Luttmann, Edgar AU - Ensign, Daniel AU - Vaidyanathan, Vishal AU - Houston, Mike AU - Rimon, Noam AU - Øland, Jeppe AU - Jayachandran, Guha AU - Friedrichs, Mark AU - Pande, Vijay PY - 2009/// UR - http://dx.doi.org/10.1002/jcc.21054 ER -