A direct multiple histogram reweighting method for optimal computation of the density of states

Journal of Chemical Physics

Volumn 129, Issue 12, 2008, Pages

  Fenwick, Michael K ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; ERRORS; FINANCIAL DATA PROCESSING; ISING MODEL; KETONES; PHASE EQUILIBRIA; STATE SPACE METHODS;

AVERAGE ERRORS; BOLTZMANN ENTROPY; CONVENTIONAL APPROACH; DENSITY OF STATES; GRAND CANONICAL; ISING SPINS; MONTE CARLO; NON UNIFORM; NON-PARAMETRIC; NUMERICAL PROBLEMS; OPTIMAL COMPUTATION; POLYALANINE; REPLICA EXCHANGE; REWEIGHTING METHOD; STATE DENSITIES; STATE SPACE DISCRETIZATION; STATISTICAL ERRORS; THERMODYNAMIC FUNCTIONS; VAPOR-LIQUID EQUILIBRIUM;

SYSTEMATIC ERRORS;

PEPTIDE; POLYALANINE; UNCLASSIFIED DRUG;

ARTICLE; CHEMISTRY; MONTE CARLO METHOD; QUANTUM THEORY; VOLATILIZATION;

MONTE CARLO METHOD; PEPTIDES; QUANTUM THEORY; VOLATILIZATION;

EID: 52949130165     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2981800     Document Type: Article

References (75)

1. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953).
2. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
3. F. A. Escobedo and J. J. de Pablo, J. Chem. Phys. 105, 4391 (1996).
4. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Academic, San Diego, 1996).
5. B. J. Berne and J. E. Straub, Curr. Opin. Struct. Biol. 7, 181 (1997).
6. F. A. Escobedo, J. Chem. Phys. 108, 8761 (1998).
7. R. M. Levy and E. Gallicchio, Annu. Rev. Phys. Chem. 49, 531 (1998).
8. J. J. de Pablo, Q. Yan, and F. A. Escobedo, Annu. Rev. Phys. Chem. 50, 377 (1999).
9. A. Z. Panagiotopoulos, J. Phys.: Condens. Matter 12, R25 (2000).
10. Y. Iba, Int. J. Mod. Phys. C 12, 623 (2001).
11. A. Mitsutake, Y. Sugita, and Y. Okamoto, Biopolymers 60, 96 (2001).
12. M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002).
13. A. D. Bruce and N. B. Wilding, Adv. Chem. Phys. 127, 1 (2003).
14. D. A. Kofke, Mol. Phys. 102, 405 (2004).
15. D. J. Earl and M. W. Deem, Phys. Chem. Chem. Phys. 7, 3910 (2005).
16. D. A. Kofke, Fluid Phase Equilib. 228, 41 (2005).
17. D. P. Landau and K. Binder, A guide to Monte Carlo methods in statistical physics, 2nd ed. (Cambridge University Press, Cambridge, 2005).
18. Free energy calculations, edited by, C. Chipot, and, A. Pohorille, (Springer, New York, 2007).
19. Y. Sugita, A. Mitsutake, and Y. Okamoto, Lect. Notes Phys. 736, 369 (2008).
20. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988).
21. A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett. 63, 1195 (1989).
22. Z. W. Salsburg, J. D. Jacobson, W. Fickett, and W. W. Wood, J. Chem. Phys. 30, 65 (1959).
23. I. R. Mcdonald and K. Singer, Discuss. Faraday Soc. 43, 40 (1967).
24. J. P. Valleau and D. N. Card, J. Chem. Phys. 57, 5457 (1972).
25. C. H. Bennett, J. Comput. Phys. 22, 245 (1976).
26. M. Falcioni, E. Marinari, M. L. Paciello, G. Parisi, and B. Taglienti, Phys. Lett. 108B, 331 (1982).
27. P. Labastie and R. L. Whetten, Phys. Rev. Lett. 65, 1567 (1990).
28. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
29. J. Ferkinghoff-Borg, Eur. Phys. J. B 29, 481 (2002).
30. M. S. Shell, A. Z. Panagiotopoulos, and A. Pohorille, Free Energy Calculations, edited by, C. Chipot, and, A. Pohorille, (Springer, New York, 2007).
31. G. R. Smith and A. D. Bruce, J. Phys. A 28, 6623 (1995).
32. P. M. C. de Oliveira, T. J. P. Penna, and H. J. Herrmann, Eur. Phys. J. B 1, 205 (1998).
33. M. Fitzgerald, R. R. Picard, and R. N. Silver, Europhys. Lett. 46, 282 (1999).
34. J. S. Wang, T. K. Tay, and R. H. Swendsen, Phys. Rev. Lett. 82, 476 (1999).
35. M. Fitzgerald, R. R. Picard, and R. N. Silver, J. Stat. Phys. 98, 321 (2000).
36. J. S. Wang and R. H. Swendsen, J. Stat. Phys. 106, 245 (2002).
37. J. R. Errington, J. Chem. Phys. 118, 9915 (2003).
38. J. R. Errington, Phys. Rev. E 67, 012102 (2003).
39. M. K. Fenwick and F. A. Escobedo, J. Chem. Phys. 119, 11998 (2003).
40. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, J. Chem. Phys. 119, 9406 (2003).
41. M. K. Fenwick and F. A. Escobedo, J. Chem. Phys. 120, 3066 (2004).
42. F. A. Escobedo and C. R. A. Abreu, J. Chem. Phys. 124, 104110 (2006).
43. M. K. Fenwick, J. Chem. Phys. 125, 144905 (2006).
44. R. G. Ghulghazaryan, S. Hayryan, and C. K. Hu, J. Comput. Chem. 28, 715 (2007).
45. C. J. Geyer, in Computing Science and Statistics, Proceedings of the 23rd Symposium on the Interface, edited by, E. M. Keramidas, (Interface Foundation, Fairfax Station, VA, 1991).
46. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
47. P. R. Bevington and D. K. Robinson, Data Reduction and Error Analysis for the Physical Sciences, 2nd. ed. (McGraw-Hill, New York, 1992).
48. H. Muller-Krumbhaar and K. Binder, J. Stat. Phys. 8, 1 (1973).
49. A. M. Ferrenberg, D. P. Landau, and R. H. Swendsen, Phys. Rev. E 51, 5092 (1995).
50. J. D. Chodera, W. C. Swope, J. W. Pitera, C. Seok, and K. A. Dill, J. Chem. Theory Comput. 3, 26 (2007).
51. A. E. Ferdinand and M. E. Fisher, Phys. Rev. 185, 832 (1969).
52. P. D. Beale, Phys. Rev. Lett. 76, 78 (1996).
53. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
54. P. Ferrara, J. Apostolakis, and A. Caflisch, Proteins: Struct., Funct., Genet. 46, 24 (2002).
55. T. Lazaridis and M. Karplus, Proteins: Struct., Funct., Genet. 35, 133 (1999).
56. M. K. Fenwick and F. A. Escobedo, Biopolymers 68, 160 (2003).
57. A. Kone and D. A. Kofke, J. Chem. Phys. 122, 206101 (2005).
58. N. Rathore, M. Chopra, and J. J. de Pablo, J. Chem. Phys. 122, 024111 (2005).
59. S. Duane, A. D. Kennedy, B. J. Pendleton, and D. Roweth, Phys. Lett. B 195, 216 (1987).
60. B. Mehlig, D. W. Heermann, and B. M. Forrest, Phys. Rev. B 45, 679 (1992).
61. V. Daggett and M. Levitt, J. Mol. Biol. 223, 1121 (1992).
62. A. Mitsutake and Y. Okamoto, J. Chem. Phys. 112, 10638 (2000).
63. J. A. Vila, D. R. Ripoll, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 97, 13075 (2000).
64. Y. Levy, J. Jortner, and O. M. Becker, Proc. Natl. Acad. Sci. U.S.A. 98, 2188 (2001).
65. Y. Peng and U. H. E. Hansmann, Biophys. J. 82, 3269 (2002).
66. H. D. Nguyen, A. J. Marchut, and C. K. Hall, Protein Sci. 13, 2909 (2004).
67. S. Gnanakaran and A. E. Garcia, Proteins: Struct., Funct., Bioinf. 59, 773 (2005).
68. M. N. Kobrak, J. Comput. Chem. 24, 1437 (2003).
69. D. W. Scott, Biometrika 66, 605 (1979).
70. D. Freedman and P. Diaconis, Z. Wahrscheinlichkeitstheor. Verwandte Geb. 57, 453 (1981).
71. D. W. Scott, Multivariate Density Estimation (Wiley, New York, 1992).
72. M. P. Wand, Am. Stat. 51, 59 (1997).
73. Q. Yan and J. J. de Pablo, J. Chem. Phys. 111, 9509 (1999).
74. D. J. Adams, Mol. Phys. 29, 307 (1975).
75. J. K. Johnson, J. A. Zollweg, and K. E. Gubbins, Mol. Phys. 78, 591 (1993).