Multiple grid methods for classical molecular dynamics

Journal of Computational Chemistry

Volumn 23, Issue 6, 2002, Pages 673-684

  Skeel, Robert D ^a   Tezcan, Ismail ^a   Hardy, David J ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Fast electrostatics; Fast multipole method; Molecular dynamics; Multigrid method; N body solver

Indexed keywords

ALGORITHM; ARTICLE; CHEMICAL MODEL; MONTE CARLO METHOD; PHYSICAL CHEMISTRY; STATISTICS;

ALGORITHMS; CHEMISTRY, PHYSICAL; MODELS, CHEMICAL; MONTE CARLO METHOD;

EID: 0037197257     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10072     Document Type: Article

References (31)

1. 1 Greengard, L. ; Rokhlin, V. J Comput Phys 1987, 73, 325.
2. 2 Appel, A. W. SIAM J Sci Statist Comput 1985, 6, 85.
3. 3 Barnes, J. ; Hut, P. Nature 1986, 324, 446.
4. 4 Rankin, W. ; Board, J., 4th IEEE Symposium on High Performance Distributed Computing, Proceedings, IEEE Computer Society, 1995, p. 17.
5. 5 URL: http://www.ee.duke.edu/Research/SciComp/Docs/Dpmta.
6. 6 URL: http://www.ks.uiuc.edu/Research/namd.
7. 7 Kalé, L. ; Skeel, R. ; Brunner, R. ; Bhandarkar, M. ; Gursoy, A. ; Krawetz, N. ; Phillips, J. ; Shinozaki, A. ; Varadarajan, K. ; Schulten, K. J Comput Phys 1999, 151, 283.
8. 8 Warming, R. F. ; Hyett, B. J. J Comput Phys 1974, 14, 159.
9. 9 Griffiths, D. F. ; Sanz–Serna, J. M. SIAM J Sci Statist Comput 1986, 7, 994.
10. 10 Skeel, R. D. ; Hardy, D. J. Practical Construction of Modified Hamiltonians. SIAM J Sci Comput 2001, 23, 1172.
11. 11 Bishop, T. ; Skeel, R. D. ; Schulten, K. J Comput Chem 1997, 18, 1785.
12. 12 Sagui, C. ; Darden, T. J Chem Phys 2001, 114, 6578.
13. 13 Brandt, A. ; Lubrecht, A. A. J Comput Phys 1990, 90, 348.
14. 14 Skeel, R. D. In Multiscale Computational Methods in Chemistry and Physics, Brandt, A. ; Bernholc, J. ; Binder, K., Eds.; volume 177 of NATO Science Series: Series III Computer and Systems Sciences ; IOS Press: Amsterdam, 2001, p. 3.
15. 15 Hockney, R. W. ; Eastwood, J. W. Computer Simulation Using Particles ; McGraw‐Hill: New York, 1981.
16. 16 Sandak, B. J Comput Chem 2001, 22, 717.
17. 17 Essmann, U. ; Perera, L. ; Berkowitz, M. L. ; Darden, T. ; Lee, H. ; Pederson, L. J Chem Phys 1995, 103, 8577.
18. 18 Cheng, H. ; Greengard, L. ; Rokhlin, V. J Comput Phys 1999, 155, 468.
19. 19 Brandt, A. ; Venner, C. H. SIAM J Sci Comput 1998, 19, 468.
20. 20 Kahaner, D. ; Moler, C. ; Nash, S. Numerical Methods and Software ; Prentice‐Hall ; Englewood Cliffs, NJ, 1989.
21. 21 Duan, Z.‐H. ; Krasny, R. J Comput Chem 2001, 22, 184.
22. 22 Zaslavsky, L. Y. ; Schlick, T. Appl Math Comp 1998, 97, 237.
23. 23 Anderson, C. R. SIAM J Sci Stat Comp 1992, 13, 923.
24. 24 Makino, J. J Comput Phys 1999, 151, 910.
25. 25 Jorgensen, W. L. ; Chandrasekhar, J. ; Madura, J. D. ; Impey, R. W. ; Klein, M. L. J Chem Phys 1983, 79, 926.
26. 26 Leach, A. R. Molecular Modelling: Principles and Applications ; Addison‐Wesley Longman: Reading, MA, 1996.
27. 27 Grubmüller, H. ; Heller, H. ; Windemuth, A. ; Schulten, K. Mol Simulat 1991, 6, 121.
28. 28 Tuckerman, M. ; Berne, B. J. ; Martyna, G. J. J Chem Phys 1992, 97, 1990.
29. 29 Skeel, R. D. ; Biesiadecki, J. J. Ann Numer Math 1994, 1, 191.
30. 30 Fox, G. C. ; Johnson, M. A. ; Lyzenga, G. A. ; Otto, S. W. ; Salmon, J. K. ; Walker, D. W. Solving Problems on Concurrent Processors, Volume I: General Techniques and Regular Problems ; Prentice‐Hall: Englewood Cliffs, NJ, 1988.
31. 31 Brooks, B. April 2000. Personal communication.