Computing bounds on free energy changes with one and two dimensional paths

Journal of Physical Chemistry B

Volumn 101, Issue 45, 1997, Pages 9402-9409

  Jarque, Cristina ^a   Tidor, Bruce ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; CONVERGENCE OF NUMERICAL METHODS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS;

HAMILTONIAN SWITCHING SIMULATION; SOLVATION ENERGY;

FREE ENERGY;

EID: 0031556559     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9716795     Document Type: Article

References (30)

1. Beveridge, D. L.; DiCapua, F. M. Free energy via molecular simulation: Applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492.
2. Jorgensen, W. L. Free energy calculations: A breakthrough for modeling organic chemistry in solution. Acc. Chem. Res. 1989, 22, 184-189.
3. Kollman, P. A.; Merz, K. M., Jr. Computer modeling of the interactions of complex molecules. Acc. Chem. Res. 1990, 23, 246-252.
4. van Gunsteren, W. F.; Berendsen, H. J. C. Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry. Angew. Chem., Int. Ed. Engl. 1990, 29, 992-1023.
5. McCammon, J. A. Free energy from simulations. Curr. Opin. Struct. Biol. 1991, 1, 196-200.
6. Straatsma, T. P.; McCammon, J. A. Chemical alchemy. Annu. Rev. Phys. Chem. 1992, 43, 407-435.
7. Kollman, P. A. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
8. Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 1954, 22, 1420-1426.
9. Kirkwood, J. G. In Theory of Liquids; Alder, B. J., Ed.; Gordon & Breach: New York, 1968.
10. Singh, U. C.; Brown, F. K.; Bash, P. A.; Kollman, P. A. An approach to the application of free energy perturbation methods using molecular dynamics. J. Am. Chem. Soc. 1987, 109, 1607-1614.
11. van Gunsteren, W. F. Methods for calculation of free energies and binding constants: Successes and problems. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; van Gunsteren, W. F., Weiner, P. K., Ed.; ESCOM: Leiden, 1989; pp 27-59.
12. Watanabe, M.; Reinhardt, W. P. Direct dynamical calculation of entropy and free energy by adiabatic switching. Phys. Rev. Lett. 1990, 65, 3301-3304.
13. Reinhardt, W. P.; Hunter, J. E., III. Variational path optimization and upper and lower bounds to free energy changes via finite time minimization of external work. J. Chem. Phys. 1992, 97, 1599-1601.
14. Hunter, J. E., III, Reinhardt, W. P.; Davis, T. F. A finite-time variational method for determining optimal paths and obtaining bounds on free energy changes from computer simulations. J. Chem. Phys. 1993, 99, 6856-6864.
15. Mark, A. E.; van Gunsteren, W. F.; Berendsen, H. J. C. Calculation of relative free energy via indirect pathways. J. Chem. Phys. 1991, 94, 3808-3816.
16. Mezei, M.; Beveridge, D. L. Free energy simulations. In Computer Simulation of Chemical and Biomolecular Systems; Beveridge, D. L.; Jorgensen, W. L., Ed.; New York Academy of Sciences: New York, 1986; pp 1-23.
17. Simonson, T. Free energy of particle insertion. An exact analysis of the origin singularity for simple liquids. Mol. Phys. 1993, 80, 441-447.
18. Resat, H.; Mezei, M. Studies on free energy calculations. II. A theoretical approach to molecular solvation. J. Chem. Phys. 1994, 222, 6126-6140.
19. Beutler, T. Mark, A. E.; van Schaik, R. C.; Gerber, P.; van Gunsteren, W. F. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 1994, 222, 529-539.
20. Brooks, C. L., III; Karplus, M. Solvent effects on protein motion and protein effects on solvent motion: Dynamics of the active site region of lysozyme. J. Mol. Biol. 1989, 208, 159-181.
21. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935.
22. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 1983, 187-217.
23. Tembe, B. L.; McCammon, J. A. Ligand - receptor interactions. Comput. Chem. 1984, 8, 281-283.
24. Brooks, C. L., III. Thermodynamics of ionic solvation: Monte Carlo simulations of aqueous chloride and bromide ions. J. Phys. Chem. 1986, 90, 6680-6684.
25. Tidor, B. Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte Carlo approach. J. Phys. Chem. 1993, 97, 1069-1073.
26. Jorgensen, W. L.; Ravimohan, C. Monte Carlo simulation of differences in free energies of hydration. J. Chem. Phys. 1985, 83, 3050-3054.
27. Fleischman, S. H.; Brooks, C. L., III. Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes. J. Chem. Phys. 1987, 87, 3029-3037.
28. Jarque, C.; Tidor, B. Simulated annealing on coupled free energy surfaces: Relative solvation energies of small molecules. J. Phys. Chem. B 1997, 101, 9362.
29. Taylor, J. R. An Introduction to Error Analysis; University Science Books: Mill Valley, CA 1982.
30. Kong, X.; Brooks, C. L., III. λ-dynamics: A new approach to free energy calculations. J. Chem. Phys. 1996, 105, 2414-2423.