Sampling potential energy surface of glycyl glycine peptide: Comparison of metropolis Monte Carlo and stochastic dynamics

Journal of Computational Chemistry

Volumn 19, Issue 11, 1998, Pages 1294-1299

  Senderowitz, Hanoch ^a   Still, W Clark ^a  

^a Columbia University ^*  (United States)

Author keywords

Free energy simulation; Molecular dynamics; Monte Carlo; Simulation convergence

Indexed keywords

EID: 0009724176     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199808)19:11<1294::AID-JCC9>3.0.CO;2-F     Document Type: Review

References (31)

1. M. P. Allen and D. J. Tildesley, Computer Simulations of Liquids, Clarendon Press, Oxford, U.K., 1987.
2. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. Teller, and E. Teller, J. Chem. Phys., 21, 1087 (1953).
3. S. A. Northrup and J. A. McCammon, Biopolymers, 19, 1001 (1980).
4. F. Guarnieri and W. C. Still, J. Comput. Chem., 15, 1302 (1994).
5. W. L. Jorgensen and J. Tirado-Rives, J. Phys. Chem. 100, 14508 (1996).
6. (a) W. L. Jorgensen, J. Phys. Chem., 87, 5304 (1983);
7. (b) C. L. Brooks III, B. M. Pettitt, and M. Karplus, Adv. Chem. Phys., 71, 1 (1988);
8. (c) P. A. Kollman, Chem Rev., 93, 2395 (1993);
9. (d) M. J. Mitchell and J. A. McCammon, J. Comput. Chem. 12, 271 (1991);
10. (e) W. F. van Gunsteren and A. E. Mark, Eur. J. Biochem., 204, 947 (1992);
11. (f) A. E. Mark, S. P. van Helden, P. E. Smith, L. H. M. Janssen, and W. F. van Gunsteren, J. Am. Chem. Soc., 116, 6293 (1994).
12. F. Mohamadi, N. G. J. Richards, W. C. Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson, W. C. Still, J. Comput. Chem., 11, 440 (1990).
13. S. J. Weiner, P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984).
14. J. M. Goodman and W. C. Still, J. Comput. Chem., 12, 1110 (1991).
15. E. L. Eliel and S. H. Wilen, Stereochemistry of Organic Compounds, Wiley, New York, 1994, p. 635.
16. W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes, Cambridge University Press, New York, 1986, p. 455.
17. (a) M. Rao, C. Pangali, and B. Berne, J. Mol. Phys. 37, 1773 (1979);
18. (b) C. Pangali, M. Rao, B. Berne, J. Chem. Phys. Lett. 55, 413 (1978);
19. (c) M. Rao and B. J. Gerne, J. Chem. Phys., 71, 129 (1979);
20. (d) J. Cao and B. J. Berne, J. Chem. Phys. 92, 1980 (1990);
21. (e) P. J. Rossky, J. D. Doll, and H. L. Friedman, J. Chem. Phys., 69, 4628 (1978);
22. (f) S. Goldman, J. Chem. Phys., 79, 3938 (1983);
23. (g) M. Mezei, K. A. Bencsath, S. Goldman, and S. Singh, Mol. Simul., 1, 87 (1987);
24. (h) M. J. Kotelyanskii and U. W. Suter, J. Chem. Phys., 96, 5383 (1992);
25. (i) T. Noguti and N. Go, Biopolymers, 24, 527 (1985);
26. (j) R. Abagyan and M. Totrov, J. Mol. Biol. 235, 983 (1994);
27. (k) M. E. Clamp, P. G. Baker, C. J. Stirling, and A. Brass, J. Comput. Chem. 15, 838 (1994).
28. (a) H. Senderowitz, F. Guarnieri and W. C. Still, J. Am. Chem. Soc., 117, 8211 (1995);
29. (b) H. Senderowitz, C. Parish, and W. C. Still, J. Am. Chem. Soc. 118, 2078 (1996);
30. (c) H. Senderowitz and W. C. Still, J. Phys. Chem. B, 101, 1409 (1997);
31. (d) H. Senderowitz and W. C. Still, J. Org. Chem., 62, 1427 (1997).