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Volumn 28, Issue 1-2, 2002, Pages 67-80

Reversibility of free energy simulations: Slow growth may have a unique advantage. (With a note on use of Ewald summation)

Author keywords

Accuracy; Ewald summation; Free energy; Integration method; Molecular dynamics; Slow growth

Indexed keywords

COMPUTER SIMULATION; ERROR ANALYSIS; GROWTH KINETICS; MOLECULAR DYNAMICS; PARAMETER ESTIMATION; STATISTICAL METHODS; THERMODYNAMICS;

EID: 0042531222     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020211971     Document Type: Review
Times cited : (30)

References (34)
  • 1
    • 0011389160 scopus 로고
    • Free energy via molecular simulation: A primer
    • van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden
    • Beveridge, D. L. and DiCapua, F. M., "Free energy via molecular simulation: A primer", In: Computer Simulations of Biomolecular Systems, van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden, 1989, pp. 1-26.
    • (1989) Computer Simulations of Biomolecular Systems , pp. 1-26
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 2
    • 0002531265 scopus 로고
    • Methods for calculation of free energies and binding constants: Successes and problems
    • van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden, The Netherlands
    • van Gunsteren, W. F., "Methods for calculation of free energies and binding constants: Successes and problems", In: Computer simulations of biomolecular systems, van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden, The Netherlands, 1989, pp. 27-59.
    • (1989) Computer Simulations of Biomolecular Systems , pp. 27-59
    • Van Gunsteren, W.F.1
  • 3
    • 6844227890 scopus 로고
    • Free energy perturbation calculations: Problems and pitfalls along the gilded road
    • van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden
    • Pearlman, D. A. and Kollman, P. A., "Free energy perturbation calculations: Problems and pitfalls along the gilded road", In: Computer Simulations of Biomolecular Systems, van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden, 1989, pp. 101-119.
    • (1989) Computer Simulations of Biomolecular Systems , pp. 101-119
    • Pearlman, D.A.1    Kollman, P.A.2
  • 4
    • 0003495725 scopus 로고
    • Thermodynamic calculations in biological systems
    • van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden
    • Brooks, C. L., "Thermodynamic calculations in biological systems", In: Computer simulations of biomolecular systems, van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden, 1989, pp. 73-88.
    • (1989) Computer Simulations of Biomolecular Systems , pp. 73-88
    • Brooks, C.L.1
  • 5
    • 0003475941 scopus 로고
    • Free energies in solution: The aqua vitae of computer simulations
    • van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden
    • Jorgensen, W. L., "Free energies in solution: The aqua vitae of computer simulations", In: Computer simulations of biomolecular systems, van Gunsteren, W. F. and Weiner, P. K. Eds., ESCOM: Leiden, 1989, pp. 60-71.
    • (1989) Computer Simulations of Biomolecular Systems , pp. 60-71
    • Jorgensen, W.L.1
  • 6
    • 0000152754 scopus 로고
    • A guide to Monte Carlo for statistical mechanics
    • Berne, B. J. Ed., Plenum press: New York
    • Valleau, J. P. and Torrie, G. M., "A guide to Monte Carlo for statistical mechanics", In: Statistical Mechanics. Part A: Equilibrium techniques, Berne, B. J. Ed., Plenum press: New York, 1977, pp. 169-194.
    • (1977) Statistical Mechanics. Part A: Equilibrium Techniques , pp. 169-194
    • Valleau, J.P.1    Torrie, G.M.2
  • 7
    • 33845377761 scopus 로고
    • Monte Carlo determination of the free energy and internal energy of hydration for the Ala dipeptide at 25°C
    • Mezei, M., Mehrotra, P. K. and Beveridge, D. L. (1985). "Monte Carlo determination of the free energy and internal energy of hydration for the Ala dipeptide at 25°C", J. Am. Chem. Soc., 107, 2239-2245.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 2239-2245
    • Mezei, M.1    Mehrotra, P.K.2    Beveridge, D.L.3
  • 9
    • 33845377175 scopus 로고
    • Monte Carlo simulations of alkanes in water: Hydration numbers and hydrophobic effect
    • Jorgensen, W. L., Gao, J. and Ravimohan, C. (1985). "Monte Carlo simulations of alkanes in water: Hydration numbers and hydrophobic effect", J. Phys. Chem., 89, 3470-3473.
    • (1985) J. Phys. Chem. , vol.89 , pp. 3470-3473
    • Jorgensen, W.L.1    Gao, J.2    Ravimohan, C.3
  • 10
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method
    • Zwanzig, R. W. (1954). "High-temperature equation of state by a perturbation method", J. Chem. Phys., 22, 1420-1426.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 12
    • 0004504539 scopus 로고
    • Monte Carlo simulation of differences in free energies of hydration
    • Jorgensen, W. L. and Ravimohan, C. (1985). "Monte Carlo Simulation of Differences in Free Energies of Hydration", J. Chem. Phys., 83, 3050-3054.
    • (1985) J. Chem. Phys. , vol.83 , pp. 3050-3054
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 13
    • 0000871204 scopus 로고
    • Multi configuration thermodynamic integration
    • Straatsma, T. P. and McCammon, J. A. (1991). "Multi configuration thermodynamic integration", J. Chem. Phys., 95, 1175-1188.
    • (1991) J. Chem. Phys. , vol.95 , pp. 1175-1188
    • Straatsma, T.P.1    McCammon, J.A.2
  • 14
    • 0003119916 scopus 로고
    • Statistical mechanics and molecular dynamics: The calculation of free energy
    • Hermans, J. Ed.; Polycrystal Book Service: Western Springs, IL
    • Berendsen, H. J. C., Postma, J. P. M. and van Gunsteren, W. F., "Statistical mechanics and molecular dynamics: The calculation of free energy", In: Molecular Dynamics and Protein Structure, Hermans, J. Ed.; Polycrystal Book Service: Western Springs, IL, 1985, pp. 43-46.
    • (1985) Molecular Dynamics and Protein Structure , pp. 43-46
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3
  • 15
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations of biomolecules. I. The method
    • Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A. and Rosenberg, J. M. (1992). "The weighted histogram analysis method for free-energy calculations of biomolecules. I. The method", J. Comput. Chem., 13, 1011-1021.
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 16
    • 0002611483 scopus 로고
    • Estimation of statistical errors in molecular simulation calculations
    • Straatsma, T. P., Berendsen, H. J. C. and Stain, A. (1986). "Estimation of statistical errors in molecular simulation calculations", Mol. Phys., 57, 89-95.
    • (1986) Mol. Phys. , vol.57 , pp. 89-95
    • Straatsma, T.P.1    Berendsen, H.J.C.2    Stain, A.3
  • 17
    • 84986468475 scopus 로고
    • Precision of free energies calculated by molecular dynamics simulations of peptides in solution
    • Hermans, J., Yun, R. H. and Anderson, A. G. (1992). "Precision of free energies calculated by molecular dynamics simulations of peptides in solution", J. Comput. Chem., 13, 429-442.
    • (1992) J. Comput. Chem. , vol.13 , pp. 429-442
    • Hermans, J.1    Yun, R.H.2    Anderson, A.G.3
  • 18
    • 0000464094 scopus 로고
    • Variational path optimization and upper and lower bounds to free energy changes via finite time minimization of external work
    • Reinhardt, W. P. and Hunter III, J. E. (1992). "Variational path optimization and upper and lower bounds to free energy changes via finite time minimization of external work", J. Chem. Phys., 97, 1599-1601.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1599-1601
    • Reinhardt, W.P.1    Hunter III, J.E.2
  • 19
    • 0001541834 scopus 로고
    • A finite-time variational method for determining optimal paths and obtaining bounds on free energy changes from computer simulations
    • Hunter III, J. E., Reinhardt, W. P. and Davis, T. F. (1993). "A finite-time variational method for determining optimal paths and obtaining bounds on free energy changes from computer simulations", J. Chem. Phys., 99, 6856-6864.
    • (1993) J. Chem. Phys. , vol.99 , pp. 6856-6864
    • Hunter III, J.E.1    Reinhardt, W.P.2    Davis, T.F.3
  • 20
    • 33845278967 scopus 로고
    • Excess free energy of liquids from molecular dynamics simulation. Application to water models
    • Hermans, J., Pathiaseril, A. and Anderson, A. (1988). "Excess free energy of liquids from molecular dynamics simulation. Application to water models", J. Am. Chem. Soc., 110, 5982-5986.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 5982-5986
    • Hermans, J.1    Pathiaseril, A.2    Anderson, A.3
  • 21
    • 36549097253 scopus 로고
    • The lag between the Hamiltonian and the system configuration in free-energy perturbation calculations
    • Pearlman, D. A. and Kollman, P. A. (1989). "The lag between the Hamiltonian and the system configuration in free-energy perturbation calculations", J. Chem. Phys., 91, 7831-7839.
    • (1989) J. Chem. Phys. , vol.91 , pp. 7831-7839
    • Pearlman, D.A.1    Kollman, P.A.2
  • 22
    • 0000886606 scopus 로고
    • Estimation of errors in free-energy calculations due to the lag between the Hamiltonian and the system configuration
    • Wood, R. H. (1991). "Estimation of errors in free-energy calculations due to the lag between the Hamiltonian and the system configuration", J. Phys. Chem., 95, 4838-4842.
    • (1991) J. Phys. Chem. , vol.95 , pp. 4838-4842
    • Wood, R.H.1
  • 23
    • 6944235692 scopus 로고
    • A simple analysis of noise and hysteresis in free energy simulations
    • Hermans, J. (1991). "A simple analysis of noise and hysteresis in free energy simulations", J. Phys. Chem., 95, 9029-9032.
    • (1991) J. Phys. Chem. , vol.95 , pp. 9029-9032
    • Hermans, J.1
  • 24
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. (1997). "Nonequilibrium equality for free energy differences", Phys. Rev. Lett., 78, 2690-2693.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 27
  • 28
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., Ciccotti, G. and Berendsen, H. J. C. (1977). "Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes", J. Comput. Phys., 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 29
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems
    • Darden, T. A., York, D. M. and Pedersen, L. G. (1993). "Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems", J. Chem. Phys., 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.M.2    Pedersen, L.G.3
  • 31
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman, M. E., Berne, B. J. and Martyna, G. J. (1992). "Reversible multiple time scale molecular dynamics", J. Chem. Phys., 97, 1990-2001.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1990-2001
    • Tuckerman, M.E.1    Berne, B.J.2    Martyna, G.J.3
  • 33
    • 0035826435 scopus 로고    scopus 로고
    • A 'fast growth' method of computing free energy differences
    • Hendrix, D. A. and Jarzynski, C. (2001). "A 'fast growth' method of computing free energy differences", J. Chem. Phys., 114, 5974-5981.
    • (2001) J. Chem. Phys. , vol.114 , pp. 5974-5981
    • Hendrix, D.A.1    Jarzynski, C.2
  • 34
    • 0031012579 scopus 로고    scopus 로고
    • Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies
    • Resat, H., Marrone, T. J. and McCammon, J. A. (1997). "Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies", Biophys. J., 72, 522-532.
    • (1997) Biophys. J. , vol.72 , pp. 522-532
    • Resat, H.1    Marrone, T.J.2    McCammon, J.A.3


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