Exchange frequency in replica exchange molecular dynamics

Journal of Chemical Physics

Volumn 128, Issue 2, 2008, Pages

  Sindhikara, Daniel ^a,b   Meng, Yilin ^c   Roitberg, Adrian E ^a,b  

^a University of Florida ^*  (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; MATHEMATICAL MODELS; PEPTIDES;

EXCHANGE-ATTEMPT RATES; FIXED LENGTH; REPLICA EXCHANGE MOLECULAR DYNAMICS (REMD);

MOLECULAR DYNAMICS;

PEPTIDE;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; THERMODYNAMICS;

COMPUTER SIMULATION; PEPTIDES; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 38349093284     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2816560     Document Type: Article

References (62)

1. P. G. Wolynes, J. N. Onuchic, and D. Thirumalai, Science SCIEAS 0036-8075 10.1126/science.7886447 267, 1619 (1995).
2. A. Roitberg and C. Simmerling, J. Mol. Graphics Modell. JMGMFI 1093-3263 22, 317 (2004).
3. B. A. Berg and T. Neuhaus, Phys. Lett. B PYLBAJ 0370-2693 10.1016/0370-2693(91)91256-U 267, 249 (1991).
4. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.68.9 68, 9 (1992).
5. A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-Velyaminov, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.462133 96, 1776 (1992).
6. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers BIPMAA 0006-3525 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F 60, 96 (2001).
7. R. H. Swendsen and J. S. Wang, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.57.2607 57, 2607 (1986).
8. M. C. Tesi, E. J. J. v. Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. JSTPBS 0022-4715 10.1007/BF02189229 82, 155 (1996).
9. U. H. E. Hansmann, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(97)01198-6 281, 140 (1997).
10. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. JUPSAU 0031-9015 10.1143/JPSJ.65.1604 65, 1604 (1996).
11. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(99)01123-9 314, 141 (1999).
12. R. Zhou, B. J. Berne, and R. Germain, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.201543998 98, 14931 (2001).
13. A. E. Garcia and K. Sanbonmatsu, Proteins: Struct., Funct., Genet. PSFGEY 0087-3585 10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H 42, 345 (2001).
14. K. Y. Sanbonmatsu and A. E. Garcia, Proteins: Struct., Funct., Genet. PSFGEY 0087-3585 10.1002/prot.1167 46, 225 (2002).
15. D. Paschek and A. E. Garcia, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.238105 93, 238105 (2004).
16. J. W. Pitera and W. Swope, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.1330954100 100, 7587 (2003).
17. F. Rao and A. Caflisch, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1591721 119, 4035 (2003).
18. M. Cecchini, F. Rao, M. Seeber, and A. Caflisch, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1809588 121, 10748 (2004).
19. R. Zhou, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2233312100 100, 13280 (2003).
20. A. E. Garcia and J. N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2335541100 100, 13898 (2003).
21. D. v. d. Spoel and M. M. Seibert, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.238102 96, 238102 (2006).
22. S. Trebst, M. Troyer, and U. H. E. Hansmann, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2186639 124, 174903 (2006).
23. P. Brenner, C. R. Sweet, D. Von Handorf, and J. A. Izaguirre, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2436872 126, 074103 (2007).
24. D. Kofke, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1507776 117, 6911 (2002).
25. A. Kone and D. Kofke, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1917749 122, 206101 (2005).
26. N. Rathore, M. Chopra, and J. J. d. Pablo, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1831273 122, 024111 (2005).
27. C. Predescu, M. Predescu, and C. V. Ciobanu, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp045073+ 109, 4189 (2005).
28. H. Fukunishi, O. Watanabe, and S. Takana, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1472510 116, 9058 (2002).
29. P. Liu, B. Kim, R. A. Friesner, and B. J. Berne, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0506346102 102, 13749 (2005).
30. E. Lyman, F. M. Ytreberg, and D. M. Zuckerman, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.028105 96, 028105 (2006).
31. S. W. Rick, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2431807 126, 054102 (2007).
32. X. Cheng, G. Cui, V. Hornak, and C. Simmerling, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp011321f 105, 8220 (2005).
33. A. Okur, L. Wickstrom, M. Layten, R. Geney, K. Song, V. Hornak, and C. Simmerling, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct050196z 2, 420 (2006).
34. A. Okur, D. R. Roe, G. Cui, V. Hornak, and C. Simmerling, J. Chem. Theory Comput. JCTCCE 1549-9618 3, 557 (2007).
35. A. E. Roitberg, A. Okur, and C. Simmerling, J. Phys. Chem. B JPCBFK 1089-5647 111, 2415 (2007).
36. H. Li, G. Li, B. A. Berg, and W. Yang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2354157 125, 144902 (2006).
37. E. Lyman and D. M. Zuckerman, Biophys. J. BIOJAU 0006-3495 91, 164 (2006).
38. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1308516 113, 6042 (2000).
39. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(00)00999-4 329, 261 (2000).
40. W. Zhang, C. Wu, and Y. Duan, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2056540 123, 154105 (2005).
41. S. B. Opps and J. Schofield, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.63.056701 63, 056701 (2001).
42. Y. M. Rhee and V. S. Pande, Biophys. J. BIOJAU 0006-3495 84, 775 (2003).
43. J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct0502864 3, 26 (2007).
44. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 13, 1101 (1992).
45. E. Gallicchio, M. Andrec, A. K. Felts, and R. M. Levy, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp045294f 109, 6722 (2005).
46. H. Lei, C. Wu, H. Liu, and Y. Duan, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 104, 4925 (2007).
47. Y. Z. Ohkubo and C. L. Brooks III, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2334257100 100, 13916 (2003).
48. D. A. Case, T. A. Darden, I. T. E. Cheatham, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, K. M. Merz, D. A. Pearlman, M. Crowley, R. C. Walker, W. Zhang, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K. F. Wong, F. Paesani, X. Wu, S. Brozell, V. Tsui, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, P. Beroza, D. H. Mathew, C. Schafmeister, W. S. Ross, and P. A. Kollman, AMBER9, University of California, San Francisco, CA, 2006.
49. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 65, 712 (2006).
50. J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. JCTPAH 0021-9991 24, 327 (1977).
51. A. Onufriev, D. Bashford, and D. A. Case, Proteins: Struct., Funct., Bioinf. ZZZZZZ 1097-0134 55, 383 (2004).
52. A. E. Garcia, H. Herce, and D. Paschek, Annu. Rep. Comp. Chem. ZZZZZZ 1574-1400 2, 83 (2006).
53. D. J. Lockhart and P. S. Kim, Science SCIEAS 0036-8075 10.1126/science.8469972 260, 198 (1993).
54. P. A. Thompson, W. A. Eaton, and J. Hofrichter, Biochemistry BICHAW 0006-2960 10.1021/bi9704764 36, 9200 (1997).
55. I. K. Lednev, A. S. Karnoup, M. C. Sparrow, and S. A. Asher, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja003381p 123, 2388 (2001).
56. A. E. Garcia and K. Y. Sanbonmatsu, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.042496899 99, 2782 (2002).
57. H. Nymeyer and A. E. Garcia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.2232868100 100, 13934 (2003).
58. W. Kabsch and C. Sander, Biopolymers BIPMAA 0006-3525 10.1002/bip.360221211 22, 2577 (1983).
59. M. Feig, J. Karanicolas, I. Charles, and C. L. Brooks III, MMTSB Tool Set, MMTSB NIH Research Resource, The Scripps Research Institute, 2001.
60. W. Y. Yang, J. W. Pitera, W. C. Swope, and M. Gruebele, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2003.11.033 336, 241 (2004).
61. B. K. Ho and K. A. Dill, PLOS Comput. Biol. ZZZZZZ 1553-734X 2, 0228 (2006).
62. B. Ozkan, A. Wu, J. D. Chodera, and K. A. Dill, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0703700104 104, 11987 (2007).