Efficient combination of Wang-Landau and transition matrix Monte Carlo methods for protein simulations

Journal of Computational Chemistry

Volumn 28, Issue 3, 2007, Pages 715-726

  Ghulghazaryan, Ruben G ^a,b   Hayryan, Shura ^a   Hu, Chin Kun ^c  

^a INSTITUTE OF PHYSICS   (Taiwan)

^b YEREVAN PHYSICS INSTITUTE   (Armenia)

^c NONE

Author keywords

Density of states; Proteins; Statistical errors; Transition matrix Monte Carlo; TTT identities; Wang Landau algorithm

Indexed keywords

ALGORITHMS; AMINO ACIDS; COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; ERROR ANALYSIS; MONTE CARLO METHODS;

DENSITY OF STATES; STATISTICAL ERRORS; TRANSITION MATRIX MONTE CARLO; TTT IDENTITIES; WANG-LANDAU ALGORITHMS;

PROTEINS;

PEPTIDE; PROTEIN;

ALGORITHM; CHEMISTRY; COMPUTER SIMULATION; MONTE CARLO METHOD;

ALGORITHMS; COMPUTER SIMULATION; MONTE CARLO METHOD; PEPTIDES; PROTEINS;

EID: 33847656545     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20597     Document Type: Article

References (53)

1. Metropolis, N.; Rosenbluth, A. W.; Teller, A. H.; Teller, E. J Chem Phys 1953, 21, 1087.
2. Dasgupta, C.; Ma, S.-K.; Hu, C.-K. Phys Rev B 1979, 20, 3837.
3. Hu, C.-K. Phys Rev B 1992, 46, 6592.
4. Hu, C.-K.; Lin, C.-Y.; Chen, J. A. Phys Rev Lett 1995, 75, 193 and 2786 (E).
5. Hu, C.-K.; Lin, C.-Y. Phys Rev Lett 1996, 77, 8.
6. Wang, EG.; Hu, C.-K. Phys Rev E 1997, 56, 2310.
7. Hu, C.-K.; Ivashkevich, E. V.; Lin, C. Y.; Priezzhev, V. B. Phys Rev Lett 2000, 85, 4048.
8. Lin, C.-Y.; Hu, C.-K.; Hansmann, U. H. E. Phys Rev E 2001, 64, 052903.
9. Swendsen, R. H.; Wang, J. S. Phys Rev Lett 1987, 58, 86.
10. Hu, C.-K. Phys Rev B 1984, 29, 5103.
11. Hu, C.-K. Phys Rev B 1984, 29, 5109.
12. Lyubartsev, A. P.; Martsinovski, A. A.; Shevkov, S. V.; Vorontsov-Vl'yaminov, P. N. J Chem Phys 1992, 96, 1776.
13. Geyer, C. J.; Thomson, E. A. J Am Stat Assoc 1995, 90, 909.
14. Marinari, E.; Parisi, G. Euro Phys Lett 1992, 19, 451.
15. de Oliveira, P. M. C.; Penna, T. J. P.; Hermann, H. J. Braz J Phys 1996, 26, 677.
16. de Oliveira, P. M. C.; Penna, T. J. P.; Hermann, H. J. Eur Phys J B 1998, 1, 205.
17. Wang, J. -S.; Swendsen, R. H. J Stat Phys 2001, 106, 245.
18. Lee, J. Phys Rev Lett 1993, 71, 211.
19. Berg, B. A.; Neuhaus, T. Phys Lett B 1991, 267, 249.
20. Berg, B. A.; Neuhaus, T. Phys Rev Lett 1992, 68, 9.
21. Hansmann, U. H. E.; Okamoto, Yu. J Comp Chem 1993, 14, 1333.
22. Janke, W. Physica A 1998, 254, 164.
23. Wang, F. G.; Landau, D. P. Phys Rev Lett 2001, 86, 2050.
24. Wang, F. G.; Landau, D. P. Phys Rev E 2001, 64, 056101.
25. Berg, B. A. Nucl Phys B (Proc Suppl) 1998, 63A-C, 982.
26. Lin, C. Y.: Hu, C. K.; Hansmann, U. H. E. Prot Struct Func Gene 2003, 52, 436.
27. Nguyen, P. H.; Stock, G.; Mittag, E.; Hu, C.-K.; M. S. Li, M. S. Prot Struct Func Bioinform 2005, 61, 795.
28. Hansmann, U. H. E. Comp Phys Commun 2002, 147, 604.
29. Hao, M. H.; Scheraga, H. A. J Phys Chem 1994, 98, 4940.
30. Lima, A. R.: de Oliveira, P. M. C.; Penna, T. J. P. J Stat Phys 2000, 99, 691.
31. Dayal, P.; Trebst, S.; Wessel, S.; Wurtz, D.; Troyer, M.; Sabhapandit, S.; Coppersmith, S. N. Phys Rev Lett 2004, 92, 097201.
32. Zhou, Ch.; Bhatt, R. N. Phys Rev E 2005, 72, 025701.
33. Shell, M. S.; Debenedetti, P. G.; Panagiotopoulos, A. Z. J Phys Chem B 2004, 108, 19748.
34. Alder, S.; Trebst, S.; Hartmann, A. K.; Troyer, M. J Stat Mech: Theor Exp 2004, Art No 07008.
35. Lee, H. K.; Okabe, Y.; Landau, D. P. Convergence and Refinement of the Wang-Landau Algorithm, preprint cond-mat/0506555 (2005).
36. Shell, M. S.; Debenedetti, P. G.; Panagiotopoulos, A. Z. J Chem Phys 2003, 119, 9406.
37. Momany, F. A.; McGuire, R. F.; Burgess, A. W.; Scheraga, H. A. J Phys Chem 1975, 79, 2361.
38. Eisenmenger, F.; Hansmann, U. H. E.; Hayryan, Sh.; Hu, C.-K. Comp Phys Comm 2001, 138, 192.
39. Eisenmenger, F.; Hansmann, U. H. E.; Hayryan, Sh.; Hu, C.-K. Comp Phys Commun 2006, 174, 422.
40. Hayryan, S.; Hu, C.-K.: Hu, S.-Y.; Shang, R.-J. J Comp Chem 2001, 22, 1287.
41. Eisenberg, D.; McLachlan, A. D. Nature 1986, 316, 199.
42. Ooi, T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Proc Natl Acad Sci US A 1987, 8, 3036.
43. Wang, J.-S. Eur Phys J B 1999, 8, 287.
44. Wang, J.-S.; Lee, L. W. Comp Phys Comm 2000, 127, 131.
45. Press, W. H.; Teukolsky, S.A.; Vetterling, W. T.; Flannery, B. P. Numerical Recipes in Fortran. The Art of Scientific Computing, 2nd ed.; Cambridge University Press; Cambridge, England, 1992.
46. Schultz, B. J.; Binder, K.; Müller, M.; Landau, D. P. Phys Rev E 2003, 67, 067102.
47. Trebst, S.; Huse, D. A.; Troyer, M. Phys Rev E 2004, 70, 046701.
48. Newman, M. E. J.; Barkema, G. T. Monte Carlo Methods in Statistical Physics; Oxford University Press: New York, 1999; p. 84.
49. Shell, M. S.; Debenedetti, P. G.; Panagiotopoulos. A. Z. Phys Rev E 2002, 66, 056703.
50. Sokal, A., in Monte Carlo and Molecular Dynamics Simulations in Polymer Science; Binder, K. Ed. Oxford University Press: New York, 1995: p. 90.
51. Go, N.; Scheraga, H. A. Macromolecules 1970, 3, 178.
52. Wedemeyer, W. J.; Scheraga, H. A. J Comp Chem 1999, 20, 819.
53. Swendsen, R. H.; Diggs, B.; Wang, J. S.; Li, S. T.; Genovese C.; Kadane, J. B. Int J Mod Phys C 1999, 10, 1563; cond-mat/9908461.