Single-ensemble nonequilibrium path-sampling estimates of free energy differences

Journal of Chemical Physics

Volumn 120, Issue 23, 2004, Pages 10876-10879

  Ytreberg, F Marty ^a   Zuckerman, Daniel M ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY PERTURBATION; JARZNSKI RELATIONS; PATH SAMPLING; SINGLE-ENSEMBLE PROTOCOLS;

DRUG PRODUCTS; HAMILTONIANS; MATHEMATICAL MODELS; MONTE CARLO METHODS; OPTIMIZATION; PHASE EQUILIBRIA; PROTEINS; THERMAL EFFECTS;

FREE ENERGY;

BIOPOLYMER;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER;

BIOPOLYMERS; COMPUTER SIMULATION; ENERGY TRANSFER; MODELS, CHEMICAL; MODELS, MOLECULAR;

EID: 3042688939     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1760511     Document Type: Article

References (23)

1. D. M. Zuckerman and T. B. Woolf, Phys. Rev. Lett. 89, 180602 (2002).
2. J. Liphardt, S. Dumont, S. B. Smith, I. Tinoco, and C. Bustamante, Science 296, 1832 (2002).
3. S. X. Sun, J. Chem. Phys. 118, 5769 (2003).
4. C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997).
5. C. Oostenbrink and W. F. van Gunsteren, J. Comput. Chem. 24, 1730 (2003).
6. T. Z. Mordasini and J. A. McCammon, J. Phys. Chem. 104, 360 (2000).
7. G. Hummer, J. Chem. Phys. 114, 7330 (2001).
8. S. Park, F. Khalili-Araghi, E. Tajkhorshid, and K. Schulten, J. Chem. Phys. 119, 3559 (2003).
9. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande, J. Chem. Phys. 119, 5740 (2003).
10. A. R. Leach, Molecular Modelling Principles and Applications (Prentice Hall, Dorset, 2001), 2nd ed.
11. C. Sotriffer, G. Klebe, M. Stahl, and H.-J. Bohm, Burger's Medicinal Chemistry and Drug Discovery, Vol. 1 (Wiley, New York, 2003), 6th ed.
12. G. E. Crooks, Phys. Rev. E 61, 2361 (2000).
13. C. Jarzynski, Phys. Rev. E 65, 046122 (2002).
14. R. Bitetti-Putzer, W. Yang, and M. Karplus, Chem. Phys. Lett. 377, 633 (2003).
15. F. M. Ytreberg and D. M. Zuckerman (unpublished).
16. D. M. Zuckerman and T. B. Woolf, Chem. Phys. Lett. 351, 445 (2002).
17. L. R. Pratt, J. Phys. Chem. 85, 5045 (1986).
18. P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Annu. Rev. Phys. Chem. 53, 291 (2002).
19. C. Dellago, P. G. Bolhuis, F. S. Csajka, and D. Chandler, J. Chem. Phys. 108, 1964 (1998).
20. G. E. Crooks and D. Chandler, Phys. Rev. E 64, 026109 (2001).
21. D. M. Zuckerman and T. B. Woolf, J. Chem. Phys. 111, 9475 (1999).
22. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, San Diego, 1996).
23. W. Yang, R. Bitetti-Putzer, and M. Karplus, J. Chem. Phys. 120, 2618 (2004).