Accelerating molecular dynamic simulation on graphics processing units Export

@article{citeulike:4007663, abstract = {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. {\copyright} 2009 Wiley Periodicals, Inc. J Comput Chem, 2009}, address = {Department of Bioengineering, Stanford University, Stanford, California 94305; Department of Chemistry, Stanford University, Stanford, California 94305; Advanced Micro Devices, Sunnyvale, California; NVIDIA Corporation, Santa Clara, California; Department of Computer Science, Stanford University, Stanford, California 94305}, author = {Friedrichs, Mark S. and Eastman, Peter and Vaidyanathan, Vishal and Houston, Mike and Legrand, Scott and Beberg, Adam L. and Ensign, Daniel L. and Bruns, Christopher M. and Pande, Vijay S.}, citeulike-article-id = {4007663}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.21209}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19191337}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19191337}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/121677402/ABSTRACT}, doi = {10.1002/jcc.21209}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {gpu, molecular\_dynamics, simulation}, number = {6}, pages = {864--872}, posted-at = {2009-02-18 10:05:41}, priority = {2}, title = {Accelerating molecular dynamic simulation on graphics processing units}, url = {http://dx.doi.org/10.1002/jcc.21209}, volume = {30}, year = {2009} }

TY - JOUR ID - citeulike:4007663 L3 - citeulike-article-id:4007663 N2 - 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. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 IS - 6 JF - Journal of Computational Chemistry SN - 1096-987X AD - Department of Bioengineering, Stanford University, Stanford, California 94305; Department of Chemistry, Stanford University, Stanford, California 94305; Advanced Micro Devices, Sunnyvale, California; NVIDIA Corporation, Santa Clara, California; Department of Computer Science, Stanford University, Stanford, California 94305 EP - 872 TI - Accelerating molecular dynamic simulation on graphics processing units VL - 30 SP - 864 KW - gpu KW - molecular_dynamics KW - simulation AU - Friedrichs, Mark AU - Eastman, Peter AU - Vaidyanathan, Vishal AU - Houston, Mike AU - Legrand, Scott AU - Beberg, Adam AU - Ensign, Daniel AU - Bruns, Christopher AU - Pande, Vijay PY - 2009/// UR - http://dx.doi.org/10.1002/jcc.21209 ER -