[1]ALLEN M P, TILDESLEY D J. Computer simulation of liquids [M]. New York: Oxford Clarendon Press, 1991: 2-3.[2]RAPAPORT D C. The art of molecular dynamics simulation [M]. Cambridge: Cambridge University Press, 2004: 7.[3]PLIMPTON S, HENDRICKSON B. A new parallel method for molecular dynamics simulation of macromolecular systems [J]. Journal of Computational Chemistry, 1996, 17(3): 326-337.[4]KALE L, SKEEL R, BHANDARKAR M, et al. NAMD2: Greater scalability for parallel molecular dynamics [J]. Journal of Computational Physics, 1999, 151(1): 283-312.[5]BROOKS B R, BROOKS C L, III, MACKERELL A D, et al. CHARMM: The biomolecular simulation program [J]. Journal of Computational Chemistry, 2009, 30(10): 1545-1615.[6]CASE D A, CHEATHAM T E III, DARDEN T, et al. The Amber biomolecular simulation programs [J]. Journal of Computational Chemistry, 2005, 26(16): 1668-1688.[7]Message Passing Interface Forum. MPI: A message-passing interface standard, version 2.2 [M]. Stuttgart: High Performance Computing Center Stuttgart, 2009.[8]Top 500 supercomputer sites. Architecture share for 11/2010 [EB/OL]. [2010-11-11]. http://www.top500.org/stats/list/36/archtype.[9]CHORLEY M J, WALKER D W. Performance analysis of a hybrid MPI/OpenMP application on multi-core clusters [J]. Journal of Computational Science, 2010, 1(3): 168-174.[10]李鸿健,白明泽,唐红,等.混合并行技术在激光化学反应模拟中的应用[J].计算机应用,2010,30(6):1687-1689.[11]AKHTER S, ROBERTS J. Multi-core programming: Increasing performance through software multi-threading [M]. Santa Clara: Intel Corporation, 2004: 139-175.[12]CHORLEY M J, WALKER D W, GUEST M F. Hybrid message-passing and shared-memory programming in a molecular dynamics application on multicore clusters [J]. International Journal of High Performance Computing Applications, 2009, 23(3): 196-211.[13]CHAPMAN B, JOST G, van der PAS R. Using OpenMP: Portable shared memory parallel programming [M]. Cambridge: MIT Press, 2007: 23-34.[14]GUPTA S. Computing aspects of molecular dynamics simulation [J]. Computer Physics Communications, 1992, 70(2): 243-270.[15]NEITZER R H, MILLER B, P. What are race conditions? some issues and formalizations [J]. ACM Letters on Programming Languages and Systems, 1992, 1(1): 74-88.[16]BAI SHU-REN, RAN LI-PING, LU KUI-LIN. Parallelization and performance tuning of molecular dynamics code with OpenMP [J]. Journal of Central South University of Technology: English Edition, 2006, 13(3): 260-264.[17]TARMYSHOV K B, MULLER-PLATHE F. Parallelizing a molecular dynamics algorithm on a multiprocessor workstation using OpenMP [J]. Journal of Chemical Information and Modeling, 2005, 45(6): 1943-1952. |