Chapter 8 Nonequilibrium Approaches to Free Energy Calculations

Annual Reports in Computational Chemistry

Volumn 1, Issue C, 2005, Pages 103-111

  Roitberg, Adrian E ^a  

^a University of Florida ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 46449111961     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(05)01008-X     Document Type: Review

References (25)

1. Jorgensen W.L. The many roles of computation in drug discovery. Science 303 5665 (2004) 1813-1818
2. Ridder L., Rietjens I., Vervoort J., and Mulholland A.J. Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide. J. Am. Chem. Soc. 124 33 (2002) 9926-9936
3. Shirts M.R., Pitera J.W., Swope W.C., and Pande V.S. Extremely precise free energy calculations of amino acid side chain analogs: comparison of common molecular mechanics force fields for proteins. J. Chem. Phys. 119 11 (2003) 5740-5761
4. Jarzynski C. Equilibrium free-energy differences from nonequilibrium measurements: a master-equation approach. Phys. Rev. E 56 5 (1997) 5018-5035
5. Jarzynski C. Equilibrium free energies from nonequilibrium processes. Acta Phys. Pol. B 29 6 (1998) 1609-1622
6. Jarzynski C. Microscopic analysis of Clausius-Duhem processes. J. Stat. Phys. 96 1-2 (1999) 415-427
7. Jarzynski C. Hamiltonian derivation of a detailed fluctuation theorem. J. Stat. Phys. 98 1-2 (2000) 77-102
8. Jarzynski C. How does a system respond when driven away from thermal equilibrium?. Proc. Natl Acad. Sci. USA 98 7 (2001) 3636-3638
9. Zwanzig R.W. High-temperature equation of state by a perturbation method. 1. Nonpolar gases. J. Chem. Phys. 22 8 (1954) 1420-1426
10. Okamoto Y. Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model. 22 5 (2004) 425-439
11. Kinnear B.S., Jarrold M.F., and Hansmann U.H.E. All-atom generalized-ensemble simulations of small proteins. J. Mol. Graph. Model. 22 5 (2004) 397-403
12. Hermans J. Simple analysis of noise and hysteresis in (slow-growth) free-energy simulations. J. Phys. Chem. 95 23 (1991) 9029-9032
13. Onoa B., Dumont S., Liphardt J., Smith S.B., Tinoco I., and Bustamante C. Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme. Science 299 5614 (2003) 1892-1895
14. Danilowicz C., Coljee V.W., Bouzigues C., Lubensky D.K., Nelson D.R., and Prentiss M. DNA unzipped under a constant force exhibits multiple metastable intermediates. Proc. Natl Acad. Sci. USA 100 4 (2003) 1694-1699
15. Weisel J.W., Shuman H., and Litvinov R.I. Protein-protein unbinding induced by force: single-molecule studies. Curr. Opin. Struct. Biol. 13 2 (2003) 227-235
16. Wang G.M., Sevick E.M., Mittag E., Searles D.J., and Evans D.J. Experimental demonstration of violations of the second law of thermodynamics for small systems and short time scales. Phys. Rev. Lett. 89 5 (2002)
17. Evans D.J. A non-equilibrium free energy theorem for deterministic systems. Mol. Phys. 101 10 (2003) 1551-1554
18. Mittag E., and Evans D.J. Time-dependent fluctuation theorem. Phys. Rev. E 67 2 (2003)
19. Gore J., Ritort F., and Bustamante C. Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proc. Natl Acad. Sci. USA 100 22 (2003) 12564-12569
20. Hummer G., and Szabo A. Kinetics from nonequilibrium single-molecule pulling experiments. Biophys. J. 85 1 (2003) 5-15
21. Mukamel S. Quantum extension of the Jarzynski relation: analogy with stochastic dephasing. Phys. Rev. Lett. 90 17 (2003)
22. Sun S.X. Equilibrium free energies from path sampling of nonequilibrium trajectories. J. Chem. Phys. 118 13 (2003) 5769-5775
23. Dellago C., Bolhuis P.G., and Chandler D. J. Chem. Phys. 108 (1998) 9236
24. Li P.C., and Makarov D.E. Theoretical studies of the mechanical unfolding of the muscle protein titin: bridging the time-scale gap between simulation and experiment. J. Chem. Phys. 119 17 (2003) 9260-9268
25. Park S., Khalili-Araghi F., Tajkhorshid E., and Schulten K. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. J. Chem. Phys. 119 6 (2003) 3559-3566