Calculation of free-energy differences and potentials of mean force by a multi-energy gap method

Journal of Chemical Physics

Volumn 128, Issue 11, 2008, Pages

  Zhou, Huan Xiang ^a  

^a Florida State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; FREE ENERGY; HIGH TEMPERATURE OPERATIONS; MOLECULAR DYNAMICS; MONTE CARLO METHODS;

ENERGY FUNCTION; FREE-ENERGY CALCULATIONS;

ENERGY GAP;

HYDROGEN;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; ENTROPY; KINETICS; THERMODYNAMICS;

COMPUTER SIMULATION; ENERGY TRANSFER; ENTROPY; HYDROGEN; KINETICS; THERMODYNAMICS;

EID: 41049087453     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2841942     Document Type: Article

References (20)

1. For example, a recent free-energy calculation [D. Hamelberg and J. A. McCammon, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja0377908 126, 7698 (2004)] is used to help characterize protein-drug interactions.
2. J. G. Kirkwood, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1749657 3, 300 (1935).
3. R. W. Zwanzig, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1740409 22, 1420 (1954).
4. G. M. Torrie and J. P. Valleau, J. Comput. Phys. JCTPAH 0021-9991 10.1016/0021-9991(77)90121-8 23, 187 (1977).
5. C. Jarzynski, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.78. 2690 78, 2690 (1997).
6. G. Hummer and A. Szabo, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.071034098 98, 3658 (2001).
7. E. Darve and A. Pohorille, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1410978 115, 9169 (2001).
8. A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.202427399 99, 12562 (2002).
9. F. M. Ytreberg and D. M. Zuckerman, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1760511 120, 10876 (2004).
10. H. Z. Li, M. Fajer, and W. Yang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2424700 126, 024106 (2007).
11. P. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Clarendon, Oxford, 1987).
12. B. A. Berg and T. Neuhaus, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.68.9 68, 9 (1992).
13. F. Wang and D. P. Landau, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.86.2050 86, 2050 (2001).
14. B. A. Berg, H. Noguchi, and Y. Okamoto, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.68.036126 68, 036126 (2003).
15. B. A. Berg, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.90. 180601 90, 180601 (2003).
16. B. A. Berg and H.-X. Zhou, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.72.016712 72, 016712 (2005).
17. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1699114 21, 1087 (1953).
18. W. H. Press, B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling, Numerical Recipes (Cambridge University Press, London, 1986).
19. S. Kumar, J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540130812 13, 1011 (1992).
20. W. L. Jorgensen, J. D. Madura, and C. J. Swenson, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00334a030 106, 6638 (1984).