Minimizing thermodynamic length to select intermediate states for free-energy calculations and replica-exchange simulations

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

Volumn 80, Issue 4, 2009, Pages

  Shenfeld, Daniel K ^a   Xu, Huafeng ^a   Eastwood, Michael P ^a   Dror, Ron O ^a   Shaw, David E ^a,b  

^a D E SHAW RESEARCH   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL THERMODYNAMICS; DERIVE BOUNDS; EQUILIBRIUM STATE; FREE-ENERGY CALCULATIONS; FREE-ENERGY DIFFERENCE; INTERMEDIATE STATE; REPLICA EXCHANGE SIMULATION; STATISTICAL ERRORS;

FREE ENERGY; OPTIMIZATION;

THERMODYNAMICS;

EID: 70449117689     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.80.046705     Document Type: Article

References (23)

1. P. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993). 10.1021/cr00023a004
2. C. H. Bennett, J. Comput. Phys. 22, 245 (1976). 10.1016/0021-9991(76) 90078-4
3. M. R. Shirts, E. Bair, G. Hooker, and V. S. Pande, Phys. Rev. Lett. 91, 140601 (2003). 10.1103/PhysRevLett.91.140601
4. D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 90, 2460 (1989). 10.1063/1.455988
5. N. Lu and D. A. Kofke, J. Chem. Phys. 111, 4414 (1999). 10.1063/1.479206
6. R. J. Radmer and P. A. Kollman, J. Comput. Chem. 18, 902 (1997). 10.1002/(SICI)1096-987X(199705)18:7<902::AID-JCC4>3.0.CO;2-V
7. D. Wu and D. A. Kofke, J. Chem. Phys. 123, 084109 (2005). 10.1063/1.2011391
8. C. J. Geyer, in Computing Science and Statistics Proceedings of the 23rd Symposium on the Interface (American Statistical Association, New York, 1991), pp. 156-163.
9. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 113, 6042 (2000). 10.1063/1.1308516
10. H. Fukunishi, O. Watanabe, and S. Takada, J. Chem. Phys. 116, 9058 (2002). 10.1063/1.1472510
11. R. Affentranger, I. Tavernelli, and E. E. D. Iorio, J. Chem. Theory Comput. 2, 217 (2006). 10.1021/ct050250b
12. D. J. Earl and M. W. Deem, Phys. Chem. Chem. Phys. 7, 3910 (2005). 10.1039/b509983h
13. D. A. Kofke, J. Chem. Phys. 117, 6911 (2002). 10.1063/1.1507776
14. C. Predescu, M. Predescu, and C. V. Ciobanu, J. Chem. Phys. 120, 4119 (2004). 10.1063/1.1644093
15. A. Kone and D. A. Kofke, J. Chem. Phys. 122, 206101 (2005). 10.1063/1.1917749
16. N. Rathore, M. Chopra, and J. J. de Pablo, J. Chem. Phys. 122, 024111 (2005). 10.1063/1.1831273
17. C. Predescu, M. Predescu, and C. V. Ciobanu, J. Phys. Chem. B 109, 4189 (2005). 10.1021/jp045073+
18. W. Nadler and U. H. E. Hansmann, Phys. Rev. E 76, 065701 (R) (2007). 10.1103/PhysRevE.76.065701
19. F. Weinhold, J. Chem. Phys. 63, 2479 (1975). 10.1063/1.431689
20. P. Salamon and R. S. Berry, Phys. Rev. Lett. 51, 1127 (1983). 10.1103/PhysRevLett.51.1127
21. G. E. Crooks, Phys. Rev. Lett. 99, 100602 (2007). 10.1103/PhysRevLett.99. 100602
22. S.-I. Amari, Differential-Geometrical Methods in Statistics, Lecture Notes in Statistics Vol. 28 (Springer-Verlag, Berlin, Heidelberg, 1985).
23. H. G. Katzgraber, S. Trebst, D. A. Huse, and M. Troyer, J. Stat. Mech.: Theory Exp. (2006) P03018. 10.1088/1742-5468/2006/03/P03018