Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

Journal of Chemical Physics

Volumn 120, Issue 6, 2004, Pages 2618-2628

  Yang, Wei ^a   Bitetti Putzer, Ryan ^a,b   Karplus, Martin ^a,c  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITÉ LOUIS PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; COMPUTER SIMULATION; CONFORMATIONS; CONVERGENCE OF NUMERICAL METHODS; ELECTROSTATICS; ERROR ANALYSIS; HYDROPHILICITY; HYDROPHOBICITY; INTEGRATION; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION; POTENTIAL ENERGY; QUANTUM THEORY; SOLVENTS; TOPOLOGY;

ALCHEMICAL TRANSFORMATIONS; REVERSE CUMULATIVE AVERAGING (RCA); THERMAL EQUILIBRIUM;

FREE ENERGY;

ETHANE; METHANE;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; KINETICS; STATISTICAL MODEL; TIME;

CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; ETHANE; KINETICS; METHANE; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; TIME FACTORS;

EID: 1542742143     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1638996     Document Type: Article

References (45)

1. T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 35, 430 (2002).
2. C. L. III Brooks, M. Karplus, and M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics; Advance in Chemical Physics LXXI (Wiley, New York, 1988).
3. P. A. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993).
4. J. G. Kirkwood, J. Chem. Phys. 3, 300 (1935).
5. R. Zwanzig, J. Chem. Phys. 22, 1420 (1956).
6. T. Simonson, G. Archontis, and M. Karplus, J. Phys. Chem. B 41, 8347 (1997).
7. T. Simonson, G. Archontis, and M. Karplus, J. Phys. Chem. B 103, 6142 (1999).
8. S. Boresch and M. Karplus, J. Mol. Biol. 254, 801 (1995).
9. S. Boresch, G. Archontis, and M. Karplus, Proteins: Struct., Fund., Genet. 20, 25 (1994).
10. J. Wang and P. A. Kollman, J. Am. Chem. Soc. 120, 11106 (1998).
11. A. Pathiaseril and R. J. Woods, J. Am. Chem. Soc. 122, 331 (2000).
12. O. Michlelin and M. Karplus, J. Mol. Biol. 324, 547 (2002).
13. J. W. Essex, P. L. Severance, J. Tirado-Rives, and W. L. Jorgensen, J. Phys. Chem. 101, 9663 (1997).
14. V. Uspensky, Introduction to Mathematical Probability (McGraw-Hill, New York, 1937).
15. H. Flyvbjerg and H. G. Petersen, J. Chem. Phys. 91, 461 (1989).
16. G. Archontis, T. Simonson, D. Moras, and M. Karplus, J. Mol. Biol. 275, 823 (1998).
17. M. Pagano and K. Gauvreau, Principles of Biostatistics, 2nd ed. (Duxbury, Pacific Grove, CA, 2000).
18. D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 91, 7831 (1989).
19. D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 90, 2460 (1989).
20. T. P. Straatsma, H. J. C. Berendsen, and J. P. M. Postma, J. Chem. Phys. 85, 6720 (1986).
21. R. H. Wood, J. Phys. Chem. 95, 4838 (1991).
22. J. Hermans, J. Phys. Chem. 95, 9029 (1991).
23. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997).
24. D. A. Hendrix and C. Jarzynski, J. Chem. Phys. 114, 5974 (2001).
25. G. Hummer, Mol. Simul. 28, 81 (2002).
26. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon Press, Oxford, 1989).
27. S. K. Schiferl and D. C. Wallace, J. Chem. Phys. 83, 5203 (1985).
28. S. S. Shapiro and M. B. Wilk, Biometrika 52, 591 (1965).
29. S. S. Shapiro, M. B. Wilk, and H. J. Chen, J. Am. Stat. Assoc. 63, 1343 (1968).
30. R. Friedberg and J. E. Cameron, J. Chem. Phys. 52, 6049 (1970).
31. P. Royston, Stat. Comput. 2, 117 (1992).
32. S. Boresch and M. Karplus, J. Phys. Chem. A 103, 119 (1999).
33. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Phys. Chem. 79, 926 (1983).
34. E. Neria, S. Fischer, and M. Karplus, J. Chem. Phys. 105, 1902 (1996).
35. P. J. Steinbach and B. R. Brooks, J. Comput. Chem. 15, 667 (1994).
36. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984).
37. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
38. S. Boresch and M. Karplus, J. Phys. Chem. A 103, 103 (1999).
39. M. Zacharias, T. P. Straatsma, and J. A. McCammon, J. Chem. Phys. 100, 9025 (1994)
40. A. Ben-Naim and Y. J. Marcus, J. Chem. Phys. 81, 2016 (1984).
41. J. E. Davies, N. L. Doltsinis, A. J. Kirby, C. D. Roussev, and M. Sprik, J. Am. Chem. Soc. 124, 6594 (2002).
42. W. Yang, Y. Q. Gao, Q. Cui, J. Ma, and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 100, 874 (2003).
43. R. Bitetti-Putzer, W. Yang, and M. Karplus, Chem. Phys. Lett. 377, 633 (2003).
44. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002).
45. M. Brunsteiner and S. Boresch, J. Chem. Phys. 112, 6953 (2000).