Selective sampling of transition paths

Journal of Chemical Physics

Volumn 127, Issue 15, 2007, Pages

  Fu, Xuebing ^a   Yang, Lijiang ^a   Gao, Yi Qin ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; MOLECULAR DYNAMICS; NUMERICAL METHODS; PHASE SPACE METHODS; RATE CONSTANTS; THERMODYNAMIC PROPERTIES;

HIGH ENERGY BARRIERS; TRANSITION PATH SAMPLING;

PHASE TRANSITIONS;

EID: 39349096750     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2779325     Document Type: Article

References (48)

1. D. D. Frantz, D. L. Freeman, and J. D. Doll, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.458863 93, 2769 (1990).
2. C. Bartels and M. Karplus, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp972280j 102, 865 (1998).
3. E. Marinari and G. Parisi, Europhys. Lett. EULEEJ 0295-5075 10.1209/0295-5075/19/6/002 19, 451 (1992).
4. A. Mitsutake and Y. Okamoto, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(00)01262-8 332, 131 (2000).
5. U. H. E. Hansmann, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997).
6. M. Falcioni and M. W. Deem, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.477812 110, 1754 (1999).
7. Q. L. Yan and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.480282 111, 9509 (1999).
8. Q. L. Yan and J. J. de Pablo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.481905 113, 1276 (2000).
9. G. Stolovitzky and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.97.21.11164 97, 11164 (2000).
10. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999).
11. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1308516 113, 6042 (2000).
12. B. A. Berg and T. Neuhaus, Phys. Lett. B PYLBAJ 0370-2693 10.1016/0370-2693(91)91256-U 267, 249 (1991).
13. S. G. Itoh and Y. Okamoto, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2171189 124, 104103 (2006).
14. G. Bussi, A. Laio, and M. Parrinello, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.090601 96, 090601 (2006).
15. H. Grubmuller, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.52.2893 52, 2893 (1995).
16. J. Lee, H. A. Scheraga, and S. Rackovsky, J. Comput. Chem. JCCHDD 0192-8651 10.1002/(SICI)1096-987X(19970715)18:9<1222::AID-JCC10>3.0.CO;2-7 18, 1222 (1997).
17. A. F. Voter, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78. 3908 78, 3908 (1997).
18. A. F. Voter, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.473503 106, 4665 (1997).
19. L. Piela, J. Kostrowicki, and H. A. Scheraga, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100345a090 93, 3339 (1989).
20. C. H. Mak, J. Chem. Phys. JCPSA6 0021-9606 122, 214110 (2005).
21. L. D. Gelb, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1563597 118, 7747 (2003).
22. G. M. Torrie and J. P. Valleau, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(77)90121-8 23, 187 (1977).
23. D. Hamelberg, J. Mongan, and J. A. McCammon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1755656 120, 11919 (2004).
24. D. Hamelberg, T. Shen, and J. A. McCammon, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1942487 122, 241103 (2005).
25. D. Hamelberg, T. Shen, and J. A. McCammon, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja0446707 127, 1969 (2005).
26. D. Hamelberg and J. A. McCammon, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja054338a 127, 13778 (2005).
27. Y. Q. Gao and L. J. Yang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2244548 125, 114103 (2006).
28. L. J. Yang, M. P. Grubb, and Y. Q. Gao, J. Chem. Phys. JCPSA6 0021-9606 126, 125102 (2007).
29. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.475562 108, 1964 (1998).
30. P. G. Bolhuis, C. Dellago, and D. Chandler, Faraday Discuss. FDISE6 0301-7249 110, 421 (1998).
31. C. Dellago, P. G. Bolhuis, and D. Chandler, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.478569 110, 6617 (1999).
32. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. ARPLAP 0066-426X 10.1146/annurev.physchem.53.082301.113146 53, 291 (2002).
33. P. G. Bolhuis, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.1534924100 100, 12129 (2003).
34. J. Marti and F. S. Csajka, Phys. Rev. E PLEEE8 1063-651X 69, 061918 (2004).
35. T. S. van Erp, D. Moroni, and P. G. Bolhuis, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1562614 118, 7762 (2003).
36. D. Moroni, T. S. van Erp, and P. G. Bolhuis, Physica A PHYADX 0378-4371 10.1016/j.physa.2004.04.033 340, 395 (2004).
37. D. Moroni, P. G. Bolhuis, and T. S. van Erp, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1644537 120, 4055 (2004).
38. J. Hu, A. Ma, and A. R. Dinner, J. Chem. Phys. JCPSA6 0021-9606 125, 114101 (2006).
39. P. G. Bolhuis, C. Dellago, and D. Chandler, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.100127697 97, 5877 (2000).
40. R. Radhakrishnan and T. Schlick, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0308585101 101, 5970 (2004).
41. R. J. Dimelow, R. A. Bryce, A. J. Masters, I. H. Hillier, and N. A. Burton, J. Chem. Phys. JCPSA6 0021-9606 124, 114113 (2006).
42. D. A. Case, AMBER 8, University of California, San Francisco, CA, 2004.
43. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00124a002 117, 5179 (1995).
44. R. J. Woods, R. A. Dwek, C. J. Edge, and B. Fraserreid, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100011a061 99, 3832 (1995).
45. W. C. Still, A. Tempczyk, R. C. Hawley, and T. Hendrickson, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00172a038 112, 6127 (1990).
46. V. Tsui and D. A. Case, Biopolymers BIPMAA 0006-3525 10.1002/1097- 0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E 56, 275 (2000).
47. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(77)90098-5 23, 327 (1977).
48. H. J. C. Berendsen, J. P. M. Postma, W. F. Vangunsteren, A. Dinola, and J. R. Haak, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.448118 81, 3684 (1984).