An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations

Computer Physics Communications

Volumn 177, Issue 5, 2007, Pages 426-431

  Oh, Kwang Jin ^a   Deng, Yuefan ^b  

^a Korea Institute of Science and Technology Information (KISTI)   (South Korea)

^b Stony Brook University   (United States)

Author keywords

3D fast Fourier transform; Parallel molecular dynamics simulation; Smooth particle mesh Ewald method

Indexed keywords

PARALLEL COMPUTERS; PARALLEL MOLECULAR DYNAMICS SIMULATION; PERFORMANCE ANALYSIS; SMOOTH PARTICLE MESH EWALD METHOD;

ALGORITHMS; COMPUTER SIMULATION; FAST FOURIER TRANSFORMS; NUMERICAL METHODS; OPTIMIZATION; PARALLEL PROCESSING SYSTEMS;

MOLECULAR DYNAMICS;

EID: 34447503534     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2007.05.005     Document Type: Article

References (22)

1. http://www.top500.org
2. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. J. Chem. Phys. 103 (1995) 8577
3. Oh K.J., and Klein M.L. Comput. Phys. Comm. 174 (2006) 560
4. Plimpton S. J. Comp. Phys. 117 (1995) 1
5. Plimpton S., and Hendrickson B. J. Comp. Chem. 17 (1996) 326
6. Heffelfinger G.S. Comput. Phys. Comm. 128 (2000) 219
7. Oh K.J., and Klein M.L. Comput. Phys. Comm. 174 (2006) 263
8. Ryckaert J.-P., Ciccotti G., and Berendsen H.J.C. J. Comp. Chem. 23 (1977) 327
9. Andersen H.C. J. Comp. Phys. 52 (1983) 24
10. Allen M.P., and Tildesley D.J. Computer Simulation of Liquids (1987), Clarendon, Oxford
11. Eleftheriou M., Fitch B.G., Rayshubskiy A., Ward T.J.C., and Germain R.S. IBM J. Res. & Dev. 49 (2005) 457
12. Eleftheriou M., Moreira J.E., Fitch B.G., and Germain R.S. Proceedings of the Conference on High Performance Computing 194 (2003)
13. B. Fang, Y. Deng, J. Comp. Phys. (2006), accepted for publication
14. B. Fang, Y. Deng, G. Martyna, Comput. Phys. Comm. (2007), in press
15. http://www.llnl.gov/computing/tutorials/mpi_performance/
16. MacKerell Jr. A.D., et al. J. Phys. Chem. B 102 (1998) 3586
17. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926
18. http://www.fftw.org
19. Tuckerman M.E., and Martyna G.J. J. Phys. Chem. B 104 (2000) 159
20. Martyna G.J., Tuckerman M.E., Tobias D.J., and Klein M.L. Mol. Phys. 87 (1996) 1117
21. Y. Deng, A. Korobka, and B. Xiang, Int. J. High Perf. Comp. Appl. (2006), submitted for publication
22. Kake L., Skeel R., Bhandarkar M., Brunner R., Gursoy A., Krawetz N., Phillips J., Shinozaki A., Varadarajan K., and Schulten K. J. Comp. Phys. 151 (1999) 282