Enhancing systematic motion in molecular dynamics simulation

Journal of Chemical Physics

Volumn 110, Issue 19, 1999, Pages 9401-9410

  Wu, Xiongwu ^a   Wang, Shaomeng ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; ARGON; COMPUTER SIMULATION; CONFORMATIONS; CRYSTALLIZATION; EQUATIONS OF MOTION; FREE ENERGY;

CONFORMATIONAL SEARCH; SELF-GUIDED MOLECULAR DYNAMICS (SGMD) SIMULATION;

MOLECULAR DYNAMICS;

EID: 0032607091     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.478948     Document Type: Article

References (55)

1. F. Vesely, Computer Experimente an Flussigkeitsmodellen (Physik Verlag, Weinheim, 1978).
2. W. G. Hoover, Computational Statistical Mechanics (Elsevier, Amsterdam, 1991).
3. D. J. Evans and G. Morriss, Statistical Mechanics of Nonequilibrium Liquids (Academic, New York, 1990).
4. R. M. Hockey and J. W. Eastwood, Computer Simulation Using Particles (McGraw-Hill, New York, 1981).
5. D. L. Beveridge and W. L. Jorgensen, Ann. (N.Y.) Acad. Sci. 482, 1 (1986).
6. B. R. Brooks, Chem. Scr. 29A, 165 (1989).
7. M. Kaiplus and G. A. Petsko, Nature (London) 347, 631 (1990).
8. N. Metropolis and S. Vlam, J. Am. Stat. Assoc. 44, 335 (1949).
9. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
10. F. Yonezawa, Molecular Dynamics Simulations (Springer-Verlag, Berlin, 1990).
11. J. M. Haile, Molecular Dynamics Simulation-Elementary Methods (Wiley, New York, 1992).
12. M. Evans, G. J. Evans, W. T. Coffey, and P. Grigolini, Molecular Dynamics and Theory of Broad Band Spectroscopy (Wiley, New York, 1982).
13. W. G. Hoover, Annu. Rev. Phys. Chem. 34, 103 (1983).
14. W. C. Swope and H. C. Andersen, Phys. Rev. B 41, 7042 (1990).
15. D. C. Rapaport, Comput. Phys. Rep. 9, 1 (1988).
16. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
17. A. Jain, N. Vaidehi, and G. Rodriguez, J. Comput. Phys. 106, 258 (1993).
18. A. K. Mazur, V. E. Dorofeev, and R. A. Abagyan, J. Comput. Phys. 92, 261 (1991).
19. X. Wu and S. Sung, J. Comput. Chem. 19, 1555 (1998).
20. R. D. Swindoll and J. M. Haile, J. Comput. Phys. 53, 289 (1984).
21. O. Teleman and B. Jonsson, J. Comput. Chem. 7, 58 (1986).
22. M. E. Tuckerman, G. J. Martyna, and B. J. Berne, J. Chem. Phys. 93, 1287 (1990).
23. M. E. Tuckerman, B. J. Berne, and A. Rossi, J. Chem. Phys. 94, 1465 (1991).
24. M. E. Tuckerman, B. J. Berne, and G. J. Martyna, J. Chem. Phys. 94, 6811 (1991).
25. D. Janezic and B. Orel, Int. J. Quantum Chem. 51, 407 (1994).
26. S. Kirkpatrick, C. D. Gelatt, Jr., and M. P. Vecchi, Science 220, 671 (1983).
27. M. W. Johnson, Simulated Annealing and Optimization (American Science, Syracuse, 1988).
28. B. K. Lee and F. M. Richards, J. Mol. Biol. 55, 379 (1971).
29. F. M. Richards, Annu. Rev. Biophys. Bioeng. 6, 151 (1973).
30. L. Wesson and D. Eisenburg, Protein Sci. 1, 227 (1992).
31. F. H. Stillinger and D. K. Stillinger, J. Chem. Phys. 93, 6106 (1990).
32. T. Head-Gordon and F. H. Stillinger, Biopolymers 33, 293 (1993).
33. R. V. Pappu, R. K. Hart, and J. W. Ponder, J. Phys. Chem. B 102, 9725 (1998).
34. B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 7, 181 (1997).
35. X. Wu and S. Wang, J. Phys. Chem. B 102, 7238 (1998).
36. D. Thirumalai, R. D. Mountain, and T. R. Kirkpatrick, Phys. Rev. A 39, 3563 (1989).
37. R. W. Hockney, Methods Comput. Phys. 9, 136 (1970).
38. D. Potter, Computational Physics (Wiley, New York, 1972), Chap. 5.
39. W. G. Hoover, A. J. C. Ladd, and B. Moran, Phys. Rev. Lett. 48, 1818 (1982).
40. D. J. Evans, J. Chem. Phys. 78, 3297 (1983).
41. D. J. Evans and G. P. Morriss, Comput. Phys. Rep. 1, 297 (1984).
42. D. Brown and J. H. R. Clarke, Mol. Phys. 51, 1243 (1984).
43. A. Michels and H. Wijker, Physica (Amsterdam) 15, 627 (1949).
44. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
45. A. Rahman, M. J. Mandel, and J. P. McTague, J. Chem. Phys. 64, 1564 (1976).
46. F. F. Abraham, J. Chem. Phys. 72, 359 (1980).
47. C. S. Hsu and A. Rahman, J. Chem. Phys. 70, 5234 (1979).
48. J. N. Cape, J. L. Finney, and L. Woodcock, J. Chem. Phys. 75, 2366 (1981).
49. R. D. Mountain and P. K. Basu, J. Chem. Phys. 78, 7318 (1983).
50. J. D. Honeycutt and H. C. Andersen, Chem. Phys. Lett. 108, 535 (1984).
51. R. D. Mountain and A. C. Brown, J. Chem. Phys. 80, 2730 (1984).
52. S. Nose and F. Yonezawa, J. Chem. Phys. 84, 1803 (1986).
53. J. R. Melrose and K. Singer, Mol. Phys. 66, 1203 (1989).
54. I. Svishchev and P. G. Kusalik, Phys. Rev. Lett. 73, 975 (1994).
55. L. Verlet, Phys. Rev. 159, 98 (1967).