Stochastic formulation of sampling dynamics in generalized ensemble methods

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 69, Issue 2 1, 2004, Pages

  Kim, Jae Gil ^a   Fukunishi, Yoshifumi ^b   Kidera, Akinori ^c   Nakamura, Haruki ^d  

^a Japan Biological Information Research Center   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c YOKOHAMA CITY UNIVERSITY   (Japan)

^d OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION THEORY; COMPUTER SIMULATION; CONFORMATIONS; INTEGRATION; ITERATIVE METHODS; LAPLACE TRANSFORMS; MOLECULAR WEIGHT; PHASE TRANSITIONS; PROBABILITY; PROBABILITY DENSITY FUNCTION; RANDOM PROCESSES; THERMAL EFFECTS;

GENERALIZED ENSEMBLE METHODS (GEM); MULTICANONICAL SAMPLING (MUCA); PROTEIN FOLDING; SAMPLING DYNAMICS; SIMULATED TEMPERING (ST);

MOLECULAR DYNAMICS;

EID: 42749108627     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.69.021101     Document Type: Article

References (36)

1. M. Karplus and G.A. Petsko, Nature (London) 347, 631 (1990).
2. J.P.K. Doye, D.J. Wales, and M.A. Miller, J. Chem. Phys. 109, 8143 (1998).
3. C. Maranas and C. Floudas, J. Chem. Phys. 97, 7667 (1992).
4. D.D. Frantz, D.L. Freeman, and J.D. Doll, J. Chem. Phys. 93, 2769 (1990); K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
5. D.D. Frantz, D.L. Freeman, and J.D. Doll, J. Chem. Phys. 93, 2769 (1990); K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
6. J.P. Valleau, J. Chem. Phys. 99, 4718 (1993).
7. B.A. Berg and T. Neuhaus, Phys. Lett. B 267, 249 (1991).
8. J. Lee, Phys. Rev. Lett. 71, 211 (1993).
9. E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
10. A.P. Lyubartsev, A.A. Martsinovski, S.V. Shevkunov, and P.N. Vorontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992).
11. F. Wang and D.P. Landau, Phys. Rev. Lett. 86, 2050 (2001).
12. U.H.E. Hansmann, Comp. Sci. Eng. 5, 64 (2003).
13. B.A. Berg and T. Celik, Phys. Rev. Lett. 69, 2292 (1992).
14. U.H.E. Hansmann and Y. Okamoto, J. Comput. Chem. 14, 1333 (1993); N.A. Alves and U.H.E. Hansmann, J. Chem. Phys. 117, 2337 (2002).
15. U.H.E. Hansmann and Y. Okamoto, J. Comput. Chem. 14, 1333 (1993); N.A. Alves and U.H.E. Hansmann, J. Chem. Phys. 117, 2337 (2002).
16. U.H.E. Hansmann and Y. Okamoto, Phys. Rev. E 54, 5863 (1996).
17. S. Kumar, P. Payne, and M. Vasquez, J. Comput. Chem. 17, 1269 (1996).
18. C. Tsallis, J. Stat. Phys. 52, 479 (1988).
19. I. Andricioaei and J.E. Straub, Phys. Rev. E 53, 3055 (1996); J. Chem. Phys. 107, 9117 (1997).
20. I. Andricioaei and J.E. Straub, Phys. Rev. E 53, 3055 (1996); J. Chem. Phys. 107, 9117 (1997).
21. U.H.E. Hansmann and Y. Okamoto, Phys. Rev. E 56, 2228 (1997).
22. Y. Pak and S. Wang, J. Chem. Phys. 111, 4359 (1999).
23. I. Fukuda and H. Nakamura, Phys. Rev. E 65, 026105 (2002).
24. C. Beck, Phys. Rev. Lett. 87, 180601 (2001).
25. N. Nakajima, H. Nakamura, and A. Kidera, J. Phys. Chem. B 101, 817 (1997); U.H.E. Hansman, Y. Okamoto, and F. Eisenmenger, Chem. Phys. Lett. 259, 321 (1996).
26. N. Nakajima, H. Nakamura, and A. Kidera, J. Phys. Chem. B 101, 817 (1997); U.H.E. Hansman, Y. Okamoto, and F. Eisenmenger, Chem. Phys. Lett. 259, 321 (1996).
27. J.G. Kim, Y. Fukunishi, and H. Nakamura, Phys. Rev. E 67, 011105 (2003).
28. J.G. Kim, Y. Fukunishi, A. Kidera, and H. Nakamura, Phys. Rev. E 68, 021110 (2003).
29. T. Terada, Y. Matsuo, and A. Kidera, J. Chem. Phys. 118, 4306 (2003).
30. N. Rathore, T.A. Knotts IV, and J.J. de Pablo, J. Chem. Phys. 118, 4285 (2003).
31. K. Morikami, T. Nakai, A. Kidera, M. Saito, and H. Nakamura, J. Comput. Chem. 16, 243 (1992).
32. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
33. F. Yasar, T. Celik, B.A. Berg, and H. Meirovitch, J. Comput. Chem. 21, 1251 (2000); 23, 1127 (2002).
34. F. Yasar, T. Celik, B.A. Berg, and H. Meirovitch, J. Comput. Chem. 21, 1251 (2000); 23, 1127 (2002).
35. A.M. Ferrenberg and R.H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988); 63, 1195 (1989).
36. A.M. Ferrenberg and R.H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988); 63, 1195 (1989).