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Volumn 28, Issue 1-2, 2002, Pages 1-12

Free energy calculations. The long and winding gilded road

Author keywords

Convergence, of calculated free energies; Errors, of calculated free energies; Free energy calculations; Statistical simulations

Indexed keywords

COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; CONVERGENCE OF NUMERICAL METHODS; ERROR STATISTICS; NUMERICAL METHODS;

EID: 0037736706     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020211974     Document Type: Conference Paper
Times cited : (89)

References (72)
  • 1
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. (1935). Statistical mechanics of fluid mixtures, J. Chem. Phys., 3, 300-313.
    • (1935) J. Chem. Phys. , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 2
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig, R. W. (1954). High-temperature equation of state by a perturbation method. I. Nonpolar gases, J. Chem. Phys., 22, 1420-1426.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 3
    • 5244304444 scopus 로고
    • Efficient estimation of free energy differences from Monte Carlo data
    • Bennett, C. H. (1976). Efficient estimation of free energy differences from Monte Carlo data, J. Comp. Phys., 22, 245-268.
    • (1976) J. Comp. Phys. , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 4
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge, D. L. and DiCapua, F. M. (1989). Free energy via molecular simulation: Applications to chemical and biomolecular systems, Annu. Rev. Biophys. Biophys., 18, 431-492.
    • (1989) Annu. Rev. Biophys. Biophys. , vol.18 , pp. 431-492
    • Beveridge, D.L.1    Dicapua, F.M.2
  • 5
    • 0344227487 scopus 로고
    • Thermodynamics of cavity formation in water: A molecular dynamics study
    • Postma, J. P. M., Berendsen, H. J. C. and Haak, J. R. (1982). Thermodynamics of cavity formation in water: A molecular dynamics study, Faraday Symp. Chem. Soc., 17, 55-67.
    • (1982) Faraday Symp. Chem. Soc. , vol.17 , pp. 55-67
    • Postma, J.P.M.1    Berendsen, H.J.C.2    Haak, J.R.3
  • 6
    • 0007836334 scopus 로고
    • Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton transfer reactions
    • Warshel, A. (1982). Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton transfer reactions, J. Phys. Chem., 86, 2218-2224.
    • (1982) J. Phys. Chem. , vol.86 , pp. 2218-2224
    • Warshel, A.1
  • 7
    • 0023106632 scopus 로고
    • Calculation of the relative change in binding free energy of a protein-inhibitor complex
    • Bash, P. A., Singh, U. C., Brown, F. K., Langridge, R. and Kollman, P. A. (1987). Calculation of the relative change in binding free energy of a protein-inhibitor complex, Science, 235, 574-576.
    • (1987) Science , vol.235 , pp. 574-576
    • Bash, P.A.1    Singh, U.C.2    Brown, F.K.3    Langridge, R.4    Kollman, P.A.5
  • 8
    • 0021582448 scopus 로고
    • Ligand-receptor interactions
    • Tembe, B. L. and McCammon, J. A. (1984). Ligand-receptor interactions, Comp. Chem., 8, 281-283.
    • (1984) Comp. Chem. , vol.8 , pp. 281-283
    • Tembe, B.L.1    McCammon, J.A.2
  • 9
    • 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
  • 10
    • 0023346161 scopus 로고
    • Free energy calculations by computer simulation
    • Bash, P. A., Singh, U. C., Langridge, R. and Kollman, P. A. (1987). Free energy calculations by computer simulation, Science, 236, 564-568.
    • (1987) Science , vol.236 , pp. 564-568
    • Bash, P.A.1    Singh, U.C.2    Langridge, R.3    Kollman, P.A.4
  • 11
    • 0001563899 scopus 로고
    • Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations
    • Straatsma, T. P. and Berendsen, H. J. C. (1988). Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations, J. Chem. Phys., 89, 5876-5886.
    • (1988) J. Chem. Phys. , vol.89 , pp. 5876-5886
    • Straatsma, T.P.1    Berendsen, H.J.C.2
  • 12
    • 0000115003 scopus 로고
    • A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
    • Lee, F. S. and Warshel, A. (1992). A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations, J. Chem. Phys., 97, 3100-3107.
    • (1992) J. Chem. Phys. , vol.97 , pp. 3100-3107
    • Lee, F.S.1    Warshel, A.2
  • 13
    • 84913589567 scopus 로고
    • Accuracy of free energies of hydration for organic molecules from 6-31G*-derived partial charges
    • Carlson, H. A., Nguyen, T. B., Orozco, M. and Jorgensen, W. L. (1993). Accuracy of free energies of hydration for organic molecules from 6-31G*-derived partial charges, J. Comput. Chem., 14, 1240-1249.
    • (1993) J. Comput. Chem. , vol.14 , pp. 1240-1249
    • Carlson, H.A.1    Nguyen, T.B.2    Orozco, M.3    Jorgensen, W.L.4
  • 14
    • 36449000746 scopus 로고
    • Molecular dynamics free energy perturbation calculations. Influence of the truncation of long-range nonbonded interactions on the free energy of hydration of polar species
    • Chipot, C, Millot, C., Maigret, B. and Kollman, P. A. (1994). Molecular dynamics free energy perturbation calculations. Influence of the truncation of long-range nonbonded interactions on the free energy of hydration of polar species, J. Chem. Phys., 101, 7953-7962.
    • (1994) J. Chem. Phys. , vol.101 , pp. 7953-7962
    • Chipot, C.1    Millot, C.2    Maigret, B.3    Kollman, P.A.4
  • 15
    • 0026424868 scopus 로고
    • Molecular dynamics of phenol at the liquid-vapor interface of water
    • Pohorille, A. and Benjamin, I. (1991). Molecular dynamics of phenol at the liquid-vapor interface of water, J. Chem. Phys., 94, 5599-5605.
    • (1991) J. Chem. Phys. , vol.94 , pp. 5599-5605
    • Pohorille, A.1    Benjamin, I.2
  • 16
    • 0024365686 scopus 로고
    • Free energy calculations on protein stability: The Thr 157 to Val 157 mutation of T4 lysozyme
    • Merz, K. M. and Kollman, P. A. (1989). Free energy calculations on protein stability: The Thr 157 to Val 157 mutation of T4 lysozyme, J. Am. Chem. Soc., 111, 5649-5658.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 5649-5658
    • Merz, K.M.1    Kollman, P.A.2
  • 17
    • 0025319621 scopus 로고
    • Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches
    • Hirono, S. and Kollman, P. A. (1990). Calculation of the relative binding free energy of 2'GMP and 2'AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches, J. Mol. Biol., 212, 197-209.
    • (1990) J. Mol. Biol. , vol.212 , pp. 197-209
    • Hirono, S.1    Kollman, P.A.2
  • 18
    • 0025266340 scopus 로고
    • Protein-drug interactions: Characterization of inhibitor binding in complexes of dhfr with trimethoprim and related derivatives
    • Fleischman, S. H. and Brooks III, C. L. (1990). Protein-drug interactions: Characterization of inhibitor binding in complexes of dhfr with trimethoprim and related derivatives, Proteins, 7, 52-61.
    • (1990) Proteins , vol.7 , pp. 52-61
    • Fleischman, S.H.1    Brooks III, C.L.2
  • 19
    • 0008796956 scopus 로고
    • Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase
    • Cummins, P. L., Ramnarayan, K., Singh, U. C. and Gready, J. E. (1991). Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase, J. Am. Chem. Soc., 113, 8247-8256.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 8247-8256
    • Cummins, P.L.1    Ramnarayan, K.2    Singh, U.C.3    Gready, J.E.4
  • 20
    • 0025720738 scopus 로고
    • Relative differences in the binding free energies of human immunodeficiency virus 1 protease inhibitors: A thermodynamic cycle-perturbation approach
    • Reddy, M. R., Viswanadhan, V. N. and Weinstein, J. N. (1991). Relative differences in the binding free energies of human immunodeficiency virus 1 protease inhibitors: A thermodynamic cycle-perturbation approach, Proc. Natl. Acad. Sci. USA, 88, 10287-10291.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10287-10291
    • Reddy, M.R.1    Viswanadhan, V.N.2    Weinstein, J.N.3
  • 21
    • 0027239578 scopus 로고
    • What determines the strength of noncovalent association of ligands to proteins in aqueous solution?
    • Miyamoto, S. and Kollman, P. A. (1993). What determines the strength of noncovalent association of ligands to proteins in aqueous solution?, Proc. Nail. Acad. Sci. USA, 90, 8402-8406.
    • (1993) Proc. Nail. Acad. Sci. USA , vol.90 , pp. 8402-8406
    • Miyamoto, S.1    Kollman, P.A.2
  • 22
    • 0001577491 scopus 로고    scopus 로고
    • Perturbation calculations
    • Schleyer, P. V. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F. and Schreiner, P. R. (Eds.). Wiley and Sons, Chichester
    • Mark, A. E., Free Energy Perturbation Calculations. In: Encyclopedia of Computational Chemistry, Schleyer, P. V. R., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F. and Schreiner, P. R. (Eds.), Vol. 2. Wiley and Sons, Chichester, 1998, pp. 1070-1083.
    • (1998) Encyclopedia of Computational Chemistry , vol.2 , pp. 1070-1083
    • Mark, A.E.1    Energy, F.2
  • 23
    • 0001737514 scopus 로고
    • Free energy via molecular simulation: A primer
    • Van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), ESCOM, Leiden
    • King, P. M., Free energy via molecular simulation: A primer. In: Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Vol. 2, ESCOM, Leiden, 1993, pp. 267-314.
    • (1993) Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , vol.2 , pp. 267-314
    • King, P.M.1
  • 24
    • 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
  • 25
    • 0011373830 scopus 로고
    • Incomplete equilibration: A source of error in free energy calculations
    • Renugopalakrishnan, V., Carey, P. R., Smith, I. C. P., Huang, S. G. and Storer, A. C. (Eds.), ESCOM, Leiden
    • Berendsen, H. J. C., Incomplete equilibration: A source of error in free energy calculations. In: Proteins, Structure, Dynamics and Design, Renugopalakrishnan, V., Carey, P. R., Smith, I. C. P., Huang, S. G. and Storer, A. C. (Eds.), ESCOM, Leiden, 1991, pp. 384-392.
    • (1991) Proteins, Structure, Dynamics and Design , pp. 384-392
    • Berendsen, H.J.C.1
  • 26
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling
    • Torrie, G. M. and Valleau, J. P. (1977). Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling, J. Comput. Phys., 23, 187-199.
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 27
    • 36849102835 scopus 로고
    • Monte Carlo estimation of the free energy by multistage sampling
    • Valleau, J. P. and Card, D. N. (1972). Monte Carlo estimation of the free energy by multistage sampling, J. Chem. Phys., 57, 5457-5462.
    • (1972) J. Chem. Phys. , vol.57 , pp. 5457-5462
    • Valleau, J.P.1    Card, D.N.2
  • 29
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux, B. (1995). The calculation of the potential of mean force using computer simulations, Comput. Phys. Comm., 91, 275-282.
    • (1995) Comput. Phys. Comm. , vol.91 , pp. 275-282
    • Roux, B.1
  • 30
    • 0001087856 scopus 로고
    • Calculation of free energy surfaces using the methods of thermodynamic perturbation theory
    • Tobias, D. J. and Brooks III, C. L. (1987). Calculation of free energy surfaces using the methods of thermodynamic perturbation theory, Chem. Phys. Lett., 142, 472-476.
    • (1987) Chem. Phys. Lett. , vol.142 , pp. 472-476
    • Tobias, D.J.1    Brooks III, C.L.2
  • 31
    • 4344690336 scopus 로고
    • Calculations of relative free energy surfaces in configuration space using an integration method
    • Wang, C. X., Liu, H. Y., Shi, Y. Y. and Huang, F. H. (1991). Calculations of relative free energy surfaces in configuration space using an integration method, Chem. Phys. Lett., 179, 475-478.
    • (1991) Chem. Phys. Lett. , vol.179 , pp. 475-478
    • Wang, C.X.1    Liu, H.Y.2    Shi, Y.Y.3    Huang, F.H.4
  • 32
    • 0000768020 scopus 로고    scopus 로고
    • Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions
    • Chipot, C., Kollman, P. A. and Pearlman, D. A. (1996). Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions, J. Comput. Chem., 17, 1112-1131.
    • (1996) J. Comput. Chem. , vol.17 , pp. 1112-1131
    • Chipot, C.1    Kollman, P.A.2    Pearlman, D.A.3
  • 33
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free energy calculations on 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 on 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
  • 34
    • 0000764091 scopus 로고
    • Constant-temperature free energy surfaces for physical and chemical processes
    • Boczko, E. M. and Brooks III, C. L. (1993). Constant-temperature free energy surfaces for physical and chemical processes, J. Phys. Chem., 97, 4509-4513.
    • (1993) J. Phys. Chem. , vol.97 , pp. 4509-4513
    • Boczko, E.M.1    Brooks III, C.L.2
  • 35
    • 84986497803 scopus 로고
    • Multidimensional free-energy calculations using the weighted histogram analysis method
    • Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H. and Kollman, P. A. (1995). Multidimensional free-energy calculations using the weighted histogram analysis method, J. Comput. Chem., 16, 1339-1350.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kollman, P.A.5
  • 36
    • 0031595713 scopus 로고    scopus 로고
    • Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study
    • Chipot, C. and Pohorille, A. (1998). Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study, J. Phys. Chem. B, 102, 281-290.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 281-290
    • Chipot, C.1    Pohorille, A.2
  • 37
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J., Ciccotti, G. and Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion for 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.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 38
    • 36449005776 scopus 로고
    • The overlooked bond-stretching contribution in free energy perturbation calculations
    • Pearlman, D. A. and Kollman, P. A. (1991). The overlooked bond-stretching contribution in free energy perturbation calculations, J. Chem. Phys., 94, 4532-4545.
    • (1991) J. Chem. Phys. , vol.94 , pp. 4532-4545
    • Pearlman, D.A.1    Kollman, P.A.2
  • 39
    • 0001716036 scopus 로고
    • Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations
    • Straatsma, T. P., Zacharias, M. and McCammon, J. A. (1992). Holonomic constraint contributions to free energy differences from thermodynamic integration molecular dynamics simulations, Chem. Phys. Lett., 196, 297-302.
    • (1992) Chem. Phys. Lett. , vol.196 , pp. 297-302
    • Straatsma, T.P.1    Zacharias, M.2    McCammon, J.A.3
  • 40
    • 0000204832 scopus 로고    scopus 로고
    • The Jacobian factor in free energy simulations
    • Boresch, S. and Karplus, M. (1996). The Jacobian factor in free energy simulations, J. Comp. Chem., 105, 5145-5154.
    • (1996) J. Comp. Chem. , vol.105 , pp. 5145-5154
    • Boresch, S.1    Karplus, M.2
  • 41
    • 0032529893 scopus 로고    scopus 로고
    • The calculation of free-energy differences by constrained molecular dynamics simulations
    • den Otter, W. K. and Briels, W. J. (1998). The calculation of free-energy differences by constrained molecular dynamics simulations,.J. Chem. Phys., 109, 4139-4146.
    • (1998) J. Chem. Phys. , vol.109 , pp. 4139-4146
    • Den Otter, W.K.1    Briels, W.J.2
  • 42
    • 36749107785 scopus 로고
    • Molecular dynamics simulations at constant pressure and/or temperature
    • Andersen, H. C. (1980). Molecular dynamics simulations at constant pressure and/or temperature, J. Chem. Phys., 72, 2384-2393.
    • (1980) J. Chem. Phys. , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 43
    • 84926811618 scopus 로고
    • Constant pressure dynamics for molecular systems
    • Nosé, S. and Klein, M. (1983). Constant pressure dynamics for molecular systems, Mol. Phys., 50, 1055-1076.
    • (1983) Mol. Phys. , vol.50 , pp. 1055-1076
    • Nosé, S.1    Klein, M.2
  • 44
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • Nosé, S. (1984). A molecular dynamics method for simulations in the canonical ensemble, Mol. Phys., 52, 255-268.
    • (1984) Mol. Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 45
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions, Phys. Rev., A31, 1695-1697.
    • (1985) Phys. Rev. , vol.A31 , pp. 1695-1697
    • Hoover, W.G.1
  • 46
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna, G. J., Tobias, D. J. and Klein, M. L. (1994). Constant pressure molecular dynamics algorithms, J. Chem. Phys., 101, 4177-4189.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 47
    • 0002296048 scopus 로고
    • The influence of boundary conditions used in machine simulations on the structure of polar systems
    • Neumann, M. and Steinhauser, O. (1980). The influence of boundary conditions used in machine simulations on the structure of polar systems, Mol. Phys., 39, 437-54.
    • (1980) Mol. Phys. , vol.39 , pp. 437-454
    • Neumann, M.1    Steinhauser, O.2
  • 49
    • 0030163950 scopus 로고    scopus 로고
    • Ewald summation techniques in perspective: A survey
    • Toukmaji, A. Y. and Board, J. A. Jr. (1996). Ewald summation techniques in perspective: A survey, Comput. Phys. Comm., 95, 73-92.
    • (1996) Comput. Phys. Comm. , vol.95 , pp. 73-92
    • Toukmaji, A.Y.1    Board Jr., J.A.2
  • 50
    • 84977266737 scopus 로고
    • Die berechnung optischer und elektrostatischer gitterpotentiale
    • Ewald, P. (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale, Ann. Phys., 64, 253-287.
    • (1921) Ann. Phys. , vol.64 , pp. 253-287
    • Ewald, P.1
  • 51
    • 0008843911 scopus 로고
    • Reaction field, screening, and long-range interactions in simulations of ionic and dipolar systems
    • Barker, J. A. (1994). Reaction field, screening, and long-range interactions in simulations of ionic and dipolar systems, Mol. Phys., 83, 1057-1064.
    • (1994) Mol. Phys. , vol.83 , pp. 1057-1064
    • Barker, J.A.1
  • 52
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi, I. G., Sperb, R., Smith, P. E. and van Gunsteren, W. F. (1995). A generalized reaction field method for molecular dynamics simulations, J. Chem. Phys., 102, 5451 -5459.
    • (1995) J. Chem. Phys. , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 53
    • 0038683517 scopus 로고    scopus 로고
    • Ewald artifacts in computer simulations of ionic solvation and ion-ion interactions: A continuum electrostatics study
    • Hünenberger, P. H. and McCammon, J. A. (1999). Ewald artifacts in computer simulations of ionic solvation and ion-ion interactions: A continuum electrostatics study, J. Chem. Phys., 110, 1856-1872.
    • (1999) J. Chem. Phys. , vol.110 , pp. 1856-1872
    • Hünenberger, P.H.1    McCammon, J.A.2
  • 54
    • 0033726550 scopus 로고    scopus 로고
    • Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association
    • Rozanska, X. and Chipot, C. (2000). Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association, J. Chem. Phys., 112, 9691-9694.
    • (2000) J. Chem. Phys. , vol.112 , pp. 9691-9694
    • Rozanska, X.1    Chipot, C.2
  • 58
    • 0029170114 scopus 로고
    • Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins
    • Cheatham III, T. E., Miller, J. L., Fox, T., Darden, T. A. and Kollman, P. A. (1995). Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins, J. Am. Chem. Soc., 117, 4193-4194.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 4193-4194
    • Cheatham III, T.E.1    Miller, J.L.2    Fox, T.3    Darden, T.A.4    Kollman, P.A.5
  • 59
    • 33746401026 scopus 로고
    • Berendsen, H. J. C. (Ed.) (Centre Européen de Calcul Atomique et Moléculaire: Orsay, France), CECAM, workshop
    • Berendsen, H. J. C. (Ed.), MD and MC on water (Centre Européen de Calcul Atomique et Moléculaire: Orsay, France, 1972), CECAM, workshop.
    • (1972) MD and MC on Water
  • 60
    • 0001513816 scopus 로고
    • Molecular dynamics calculation of the effect of solvent polarizability on the hydrophobic interaction
    • New, M. H. and Berne, B. J. (1995). Molecular Dynamics Calculation of the Effect of Solvent Polarizability on the Hydrophobic Interaction, J. Am. Chem. Soc., 117, 7172-7179.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 7172-7179
    • New, M.H.1    Berne, B.J.2
  • 61
    • 0031341481 scopus 로고    scopus 로고
    • Effect of polarizability on the calculation of potential of mean force. The guanidinium-guanidinium ion pair in water
    • Soetens, J. C., Millot, C., Chipot, C., Jansen, G., Ángyán, J. G. and Maigret, B. (1997). Effect of polarizability on the calculation of potential of mean force. The guanidinium-guanidinium ion pair in water, J. Phys. Chem. B, 101, 10910-10917.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 10910-10917
    • Soetens, J.C.1    Millot, C.2    Chipot, C.3    Jansen, G.4    Ángyán, J.G.5    Maigret, B.6
  • 62
    • 0000371745 scopus 로고
    • Do denaturants interact with aromatic hydrocarbons in water?
    • Duffy, E. M., Kowalczyk, P. J. and Jorgensen, W. L. (1993). Do denaturants interact with aromatic hydrocarbons in water?, J. Am. Chem. Soc., 115, 9271-9275.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 9271-9275
    • Duffy, E.M.1    Kowalczyk, P.J.2    Jorgensen, W.L.3
  • 63
    • 0000299809 scopus 로고
    • Aromatic-aromatic interactions: Free energy profiles for the benzene dimer in water, chloroform and liquid benzene
    • Jorgensen, W. L. and Severance, D. L. (1990). Aromatic-aromatic interactions: Free energy profiles for the benzene dimer in water, chloroform and liquid benzene, J. Am. Chem. Soc., 112, 4768-4774.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 4768-4774
    • Jorgensen, W.L.1    Severance, D.L.2
  • 64
    • 0030062224 scopus 로고    scopus 로고
    • Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions
    • Daura, X., Hünenberger, P. H., Mark, A. E., Querol, E., Avilès, F. X. and van Gunsteren, W. F. (1996). Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions, J. Am. Chem. Soc., 118, 6285-6294.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 6285-6294
    • Daura, X.1    Hünenberger, P.H.2    Mark, A.E.3    Querol, E.4    Avilès, F.X.5    Van Gunsteren, W.F.6
  • 65
    • 0031590888 scopus 로고    scopus 로고
    • Interactions of anesthetics with the water-hexane interface. A molecular dynamics study
    • Chipot, C., Wilson, M. A. and Pohorillc, A. (1997). Interactions of anesthetics with the water-hexane interface. A molecular dynamics study, J. Phys. Chem. B, 101, 782-791.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 782-791
    • Chipot, C.1    Wilson, M.A.2    Pohorillc, A.3
  • 66
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu, S. Y., Mark, A. E. and van Gunsteren, W. F. (1996). Estimating the relative free energy of different molecular states with respect to a single reference state, J. Phys. Chem., 9485-9494, 1749.
    • (1996) J. Phys. Chem. , vol.1749 , pp. 9485-9494
    • Liu, S.Y.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 67
    • 36449009782 scopus 로고
    • Predictions of free energy differences from a single simulation of the initial state
    • Smith, P. E. and van Gunsteren, W. F. (1994). Predictions of free energy differences from a single simulation of the initial state, J. Chem. Phys., 100, 577-585.
    • (1994) J. Chem. Phys. , vol.100 , pp. 577-585
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 68
    • 0000043930 scopus 로고    scopus 로고
    • Solvation free energy of biomacromolecules: Parameters for a modified generalized born model consistent with the AMBER force field
    • Jayaram, B., Sprous, D. and Beveridge, D. L. (1998). Solvation free energy of biomacromolecules: Parameters for a modified generalized born model consistent with the AMBER force field, J. Phys. Chem. B, 102, 9571-9576.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 9571-9576
    • Jayaram, B.1    Sprous, D.2    Beveridge, D.L.3
  • 69
    • 0000249851 scopus 로고
    • Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations
    • Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R. and van Gunsteren, W. F. (1994). Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations, Chem. Phys. Lett., 222, 529-539.
    • (1994) Chem. Phys. Lett. , vol.222 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    Van Schaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5
  • 70
    • 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
  • 71
    • 6944235692 scopus 로고
    • Simple analysis of noise and hysteresis in (slow-growth) free energy simulations
    • Hermans, J. (1991). Simple analysis of noise and hysteresis in (slow-growth) free energy simulations, J. Phys. Chem., 95, 9029-9032.
    • (1991) J. Phys. Chem. , vol.95 , pp. 9029-9032
    • Hermans, J.1
  • 72
    • 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


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