Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: A general algorithm and its extension for free energy calculation on rugged energy surface

Journal of Chemical Physics

Volumn 126, Issue 11, 2007, Pages

  Li, Hongzhi ^a   Yang, Wei ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HAMILTONIAN REPLICA EXCHANGE METHOD (HREM); MOLECULAR MECHANICAL (MM) REPLICAS;

ALGORITHMS; COMPUTER SIMULATION; ELECTRONIC STRUCTURE; FREE ENERGY; MOLECULAR DYNAMICS;

QUANTUM THEORY;

EID: 34047170424     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2710790     Document Type: Article

References (63)

1. U. H. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 121 (1989);
2. M. Vasquez, G. Nemethy, and H. A. Scheraga, Chem. Rev. (Washington, D.C.) 94, 2183 (1994);
3. B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 72, 181 (1997);
4. T. Schlick, E. Barth, and M. Mand ziuk, Annu. Rev. Biophys. Biomol. Struct. 26, 181 (1997);
5. D. J. Wales and H. A. Scheraga, Science 285, 1368 (1999);
6. K. Tai, Biophys. Chem. 107, 213 (2004);
7. Y. Okamoto, J. Mol. Graphics Modell. 22, 424 (2004);
8. R. Elber, Curr. Opin. Struct. Biol. 15, 151 (2005), etc.
9. U. H. E. Hansmann and Y. Okamoto, Annu. Rev. Comput. Phys. 6, 129 (1999);
10. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers 60, 96 (2001);
11. B. A. Berg, Comput. Phys. Commun. 147, 52 (2002).
12. B. A. Berg and T. Neuhaus, Phys. Lett. B 267, 249 (1991);
13. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. 68, 9 (1992).
14. J. Lee, Phys. Rev. Lett. 71, 211 (1993).
15. Q. Yan, R. Faller, and J. J. de Pablo, J. Chem. Phys. 116, 8745 (2002).
16. F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001);
17. F. Wang and D. P. Landau, Phys. Rev. E 64, 56101 (2001).
18. A. P. Lyubartsev, A. A. Martinovski, S. V. Shevkunov, and P. N. Vortontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992);
19. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992);
20. A. Irback and F. Potthast, J. Chem. Phys. 103, 10298 (1995);
21. U. H. E. Hansmann and Y. Okamoto, Phys. Rev. E 54, 5863 (1996);
22. U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem. 18, 920 (1997);
23. E. Marinari, G. Parisi, J. J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, edited by P. Young (World Scientific, Singapore, 1998), pp. 59-98;
24. A. Irback and E. Sandelin, J. Chem. Phys. 110, 12256 (1999), etc.
25. R. H. Swendsen and F. S. Wang, Phys. Rev. Lett. 57, 2607 (1986);
26. G. F. Gerer, Stat. Sci. 7, 437 (1992);
27. K. Hukusima and K. Namoto, J. Phys. Soc. Jpn. 65, 1604 (1996);
28. U. H. Hansmann, Chem. Phys. Lett. 281, 140 (1997);
29. Y. Sugita and Y. Okamoto, ibid. 314, 141 (1999);
30. K. Y. Sanbonmatsu and A. E. Garcia, Proteins 46, 225 (2002).
31. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 113, 6042 (2000);
32. H. Fukunishi, O. Watanabe, and S. Takada, ibid. 116, 9058 (2002);
33. S. M. Jang, S. Shin, and Y. Pak, Phys. Rev. Lett. 91, 058305 (2003);
34. W. Kwak and U. H. E. Hansmann, ibid. 95, 138102 (2005);
35. P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. 102, 13749 (2005);
36. P. Liu, X. Huang, R. Zhou, and B. J. Berne, J. Phys. Chem. B 110, 19018 (2006).
37. H. Li, M. Fajer, and W. Yang, J. Chem. Phys. 126, 24106 (2007).
38. A. E. Mark, W. F. van Gunsteren, and H. J. C. Berendsen, J. Chem. Phys. 94, 3808 (1991);
39. M. de Koning, A. Antonelli, and S. Yip, Phys. Rev. Lett. 83, 3973 (1999);
40. R. Bitetti-Putzer, A. R. Dinner, W. Yang, and M. Karplus, J. Chem. Phys. 124, 174901 (2006).
41. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976);
42. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990);;
43. G. Monard and K. M. Merz, Acc. Chem. Res. 32, 904 (1999).
44. D. Min, H. Li, G. Li, R. Bitteti-Putzer, and W. Yang, J. Chem. Phys. (to be published).
45. T. Z. Lwin and R. Luo, J. Chem. Phys. 123, 194904 (2005);
46. E. Lyman, F. M. Ytreberg, and D. M. Zuckerman, Phys. Rev. Lett. 96, 28105 (2006);
47. M. Christen and W. F. van Gunsteren, J. Chem. Phys. 124, 154106 (2006).
48. W. Yang, R. Bitetti-Putzer, and M. Karplus, J. Chem. Phys. 120, 2618 (2004).
49. M. Leitgeb, C. Schroder, and S. Boresch, J. Chem. Phys. 122, 084109 (2005).
50. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
51. M. Elstner, Theor. Chem. Acc. 116, 316 (2006);
52. M. Elstner, D. Porezag, G. Jungnickel, J. Elstner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seiferr, Phys. Rev. B 58, 7260 (1998).
53. A. D. MacKerell, Jr. et al., J. Phys. Chem. B 102, 3586 (1998).
54. Y. Ishikawa, Y. Sugita, T. Nishikawa, and Y. Okamoto, Chem. Phys. Lett. 333, 199 (2001).
55. D. Frenkel and B. Smit, Understanding Molecular Simulations, 1st ed. (Academic, San Diego, 1996);
56. D. A. Kofke and P. T. Cummings, Mol. Phys. 92, 973 (1997);
57. M. Mezei, ibid. 65, 219 (1988);
58. G. L. Deitrick, L. E. Scriven, and H. T. Davis, J. Chem. Phys. 90, 2370 (1989);
59. N. Quirke, J. W. Perram, and G. Jacucci, Mol. Phys. 39, 1311 (1980);
60. K. S. Shing and K. E. Gubbins, ibid. 46, 1109 (1982).
61. S. Boresch and M. Karplus, J. Phys. Chem. A 103, 103 (1999).
62. D. M. Zuckerman and E. Lyman, J. Chem. Theory Comput. 2, 1200 (2006);
63. H. Li, G. Li, B. A. Berg, and W. Yang, J. Chem. Phys. 125, 144902 (2006).