New mean-energy formulae for free energy differences

Molecular Physics

Volumn 103, Issue 21-23 SPEC. ISS., 2005, Pages 3209-3221

  Raineri, Fernando O ^a   Stell, George ^a   Ben Amotz, Dor ^b  

^a STONY BROOK UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; PHASE TRANSITIONS; STATISTICAL MECHANICS;

FREE ENERGY CHANGE; LINEAR RESPONSE;

FREE ENERGY;

EID: 31744450875     PISSN: 00268976     EISSN: 13623028     Source Type: Journal    
DOI: 10.1080/00268970500298980     Document Type: Article

References (39)

1. R. Zwanzig. J. chem. Phys., 22, 1420 (1954).
2. D.L. Beveridge, F.M. DiCapua. Annu. Rev. Biophys. Chem., 18, 431 (1989).
3. W.L. Jorgensen. Acc. Chem. Res., 22, 184 (1989).
4. T.P. Straatsma, J.A. McCammon. Annu. Rev. Phys. Chem., 43, 407 (1992).
5. W.F. van Gunsteren, A.E. Mark. Eur. J. biochem., 204, 947 (1992).
6. C.F. Wong, J.A. McCammon. Annu. Rev. Pharmacol. Toxicol., 43, 31 (2003).
7. D. Frenkel, B. Smit. Understanding Molecular Simulation. From Algorithms to Applications, Academic Press, San Diego (1996).
8. J.G. Kirkwood. In Theory of Liquids, B.J. Alder (Ed.), Gordon & Breach, New York (1968).
9. M. Mezei. Molec. Sim., 28, 39 (2002).
10. J.W. Pitera, W.F. van Gunsteren. Molec. Sim., 28, 45 (2002).
11. J. Åqvist, C. Medina, J.-E. Samuelsson. Protein Eng., 7, 385 (1994).
12. T. Hansson, J. Marelius, J. Åqvist. J. comput.-Aided Molec. Des., 12, 27 (1998).
13. J. Åqvist, V.B. Luzhkov, B.O. Brandsdal. Acc. Chem. Res., 35, 358 (2002).
14. B.O. Bransdal, F. Oesterberg, M. Almloef, I. Feierberg, V.B. Luzhkov, J. Åqvist. Adv. Protein. Chem., 66, 123 (2003).
15. H.A. Carlson, W.L. Jorgensen. J. phys. Chem., 99, 10667 (1995).
16. N.A. McDonald, H.A. Carlson, W.L. Jorgensen. J. phys. Org. Chem., 10, 563 (1997).
17. R. Zhou, R.A. Friesner, A. Ghosh, R.C. Rizzo, W.L. Jorgensen, R.M. Levy. J. phys. Chem. B, 105, 10388 (2001).
18. D. Ostrovsky, M. Udier-Blagović, W.L. Jorgensen. J. med. Chem., 46, 5691 (2003).
19. Y. Tominaga, W.L. Jorgensen. J. med. Chem., 47, 2534 (2004).
20. I.D. Wall, A.R. Leach, D.W. Salt, M.G. Ford, J.W. Essex. J. med. Chem., 42, 5142 (1999).
21. D. Ben-Amotz, F.O. Raineri, G. Stell. J. phys. Chem. B, 109, 6866 (2005).
22. J.-P. Hansen, I.R. McDonald. Theory of Simple Liquids, 2nd edn, Academic Press, London (1990).
23. R. Kubo. J. phys. Soc. Japan, 17, 1100 (1962).
24. H. Risken. The Fokker-Planck Equation, Springer-Verlag, Berlin (1984).
25. C.W. Gardiner. Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences, Springer-Verlag, Berlin (1994).
26. P.E. Smith, W.F. van Gunsteren. J. chem. Phys., 100, 577 (1994).
27. G. Archontis, M. Karplus. J. chem. Phys., 105, 11246 (1996).
28. E.T. Whittaker, G.N. Watson. A Course of Modern Analysis, Cambridge University Press, Cambridge (1963).
29. D.V. Widder. Advanced Calculus, Dover Publications, New York (1989).
30. D. Zwillinger. Handbook of Integration, Jones and Bartlett Publishers, Boston (1992).
31. G. King, R.A. Bradford. J. phys. Chem., 97, 8798 (1993).
32. J. Aqvist, T. Hansson. J. phys. Chem., 100, 9512 (1996).
33. J.E. Hunter III, W.P. Reinhardt, T.F. Davis. J. chem. Phys., 99, 6856 (1993).
34. F.O. Raineri, B.-C. Perng, H.L. Friedman. Chem. Phys., 183, 187 (1994).
35. G. Hummer, A. Szabo. J. chem. Phys., 105, 2004 (1996).
36. R. Bürgi, F. Läng, W.F. van Gunsteren. Molec. Sim., 27, 215 (2001).
37. G.J.M. Kper, H. Reiss. J. phys. Chem., 100, 422 (1996).
38. M.R. Shirts, J.W. Pitera, W.C. Swope, V.S. Pande. J. chem. Phys., 119, 5740 (2003).
39. C.W. Wong. Introduction to Mathematical Physics: Methods and Concepts, Oxford University Press, New York (1991).