Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
作者： Kevin J Bowers , Edmond Chow , Huafeng Xu , Ron O Dror , Michael P Eastwood
DOI: 10.1109/SC.2006.54
关键词:
摘要: … Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on …
acm.org
sci-hub.se 参考文章(37)
Yong Duan, Peter A Kollman, Pathways to a Protein Folding Intermediate Observed in a 1-Microsecond Simulation in Aqueous Solution Science. ,vol. 282, pp. 740- 744 ,(1998) , 10.1126/SCIENCE.282.5389.740
Grant S. Heffelfinger, Parallel atomistic simulations Computer Physics Communications. ,vol. 128, pp. 219- 237 ,(2000) , 10.1016/S0010-4655(00)00050-3
Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, Akihiko Konagaya, Protein Explorer Proceedings of the 2003 ACM/IEEE conference on Supercomputing - SC '03. pp. 15- 15 ,(2003) , 10.1145/1048935.1050166
Jiuxing Liu, Jiesheng Wu, Sushmitha P. Kini, Pete Wyckoff, Dhabaleswar K. Panda, High performance RDMA-based MPI implementation over InfiniBand Proceedings of the 17th annual international conference on Supercomputing - ICS '03. ,vol. 32, pp. 295- 304 ,(2003) , 10.1145/782814.782855
Kevin J Bowers, Ron O Dror, David E Shaw, None, The midpoint method for parallelization of particle simulations The Journal of Chemical Physics. ,vol. 124, pp. 184109- 184109 ,(2006) , 10.1063/1.2191489
Philip M. Papadopoulos, Mason J. Katz, Greg Bruno, NPACI Rocks: tools and techniques for easily deploying manageable Linux clusters Concurrency and Computation: Practice and Experience. ,vol. 15, pp. 707- 725 ,(2003) , 10.1002/CPE.722
Steve Plimpton, Bruce Hendrickson, A new parallel method for molecular dynamics simulation of macromolecular systems Journal of Computational Chemistry. ,vol. 17, pp. 326- 337 ,(1996) , 10.1002/(SICI)1096-987X(199602)17:3<326::AID-JCC7>3.0.CO;2-X
M. Eleftheriou, B. G. Fitch, A. Rayshubskiy, T. J. C. Ward, R. S. Germain, Scalable framework for 3D FFTs on the Blue Gene/L supercomputer: implementation and early performance measurements Ibm Journal of Research and Development. ,vol. 49, pp. 457- 464 ,(2005) , 10.1147/RD.492.0457
Steve Plimpton, Fast parallel algorithms for short-range molecular dynamics Journal of Computational Physics. ,vol. 117, pp. 1- 19 ,(1995) , 10.1006/JCPH.1995.1039
A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, M. Karplus, All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B. ,vol. 102, pp. 3586- 3616 ,(1998) , 10.1021/JP973084F