메뉴 건너뛰기




Volumn 28, Issue 1-2, 2002, Pages 81-90

Fast-growth thermodynamic integration: Results for sodium ion hydration

Author keywords

Free energy perturbation theory; Ion solvation; Monte Carlo simulation; Nonequilibrium molecular dynamics

Indexed keywords

COMPUTER SIMULATION; HYDRATION; ION SOURCES; MOLECULAR DYNAMICS; MONTE CARLO METHODS; PERTURBATION TECHNIQUES; SODIUM; THERMODYNAMICS;

EID: 0002291676     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020211972     Document Type: Article
Times cited : (27)

References (51)
  • 1
    • 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.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690
    • Jarzynski, C.1
  • 2
    • 4244116139 scopus 로고    scopus 로고
    • Equilibrium free energy differences from nonequilibrium measurements. A master-equation approach
    • Jarzynski, C. (1997). "Equilibrium free energy differences from nonequilibrium measurements. A master-equation approach", Phys. Rev. E, 56, 5018.
    • (1997) Phys. Rev. E , vol.56 , pp. 5018
    • Jarzynski, C.1
  • 3
    • 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.
    • (1982) Faraday Symp. Chem. Soc. , vol.17 , pp. 55
    • Postma, J.P.M.1    Berendsen, H.J.C.2    Haak, J.R.3
  • 4
    • 36549104841 scopus 로고
    • Free energy of hydrophobic hydration. A molecular dynamics study of noble gases in water
    • Straatsma, T. P., Berendsen, H. J. C. and Postma, J. P. M. (1986). "Free energy of hydrophobic hydration. A molecular dynamics study of noble gases in water", J. Chem. Phys., 85, 6720.
    • (1986) J. Chem. Phys. , vol.85 , pp. 6720
    • Straatsma, T.P.1    Berendsen, H.J.C.2    Postma, J.P.M.3
  • 5
    • 0001563899 scopus 로고
    • Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics
    • 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", J. Chem. Phys., 89, 5876.
    • (1988) J. Chem. Phys. , vol.89 , pp. 5876
    • Straatsma, T.P.1    Berendsen, H.J.C.2
  • 7
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. (1993). "Free energy calculations: Applications to chemical and biochemical phenomena", Chem. Rev., 93, 2395.
    • (1993) Chem. Rev. , vol.93 , pp. 2395
    • Kollman, P.1
  • 8
    • 0000433021 scopus 로고
    • A new method for carrying out free energy perturbation calculations. Dynamically modified windows
    • Pearlman, D. A. and Kollman, P. A. (1989). "A new method for carrying out free energy perturbation calculations. Dynamically modified windows", J. Chem. Phys., 90, 2460.
    • (1989) J. Chem. Phys. , vol.90 , pp. 2460
    • Pearlman, D.A.1    Kollman, P.A.2
  • 9
    • 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. Comp. Chem., 17, 1112.
    • (1996) J. Comp. Chem. , vol.17 , pp. 1112
    • Chipot, C.1    Kollman, P.A.2    Pearlman, D.A.3
  • 10
    • 84986532462 scopus 로고
    • Free energy difference calculations by thermodynamic integration. Difficulties in obtaining a precise value
    • Mitchell, M. J. and McCammon, J. A. (1991). "Free energy difference calculations by thermodynamic integration. Difficulties in obtaining a precise value", J. Comp. Chem., 12, 271.
    • (1991) J. Comp. Chem. , vol.12 , pp. 271
    • Mitchell, M.J.1    McCammon, J.A.2
  • 11
    • 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.
    • (1993) J. Chem. Phys. , vol.99 , pp. 6856
    • Hunter III, J.E.1    Reinhardt, W.P.2    Davis, T.F.3
  • 12
    • 0032023968 scopus 로고    scopus 로고
    • Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems
    • Crooks, G. E. (1998). "Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems", J. Stat. Phys., 90, 1481.
    • (1998) J. Stat. Phys. , vol.90 , pp. 1481
    • Crooks, G.E.1
  • 13
    • 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.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420
    • Zwanzig, R.W.1
  • 14
    • 0042852135 scopus 로고    scopus 로고
    • Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
    • Gullingsrud, J. R., Braun, R. and Schulten, K. (1999). "Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations", J. Comp. Phys., 151, 190.
    • (1999) J. Comp. Phys. , vol.151 , pp. 190
    • Gullingsrud, J.R.1    Braun, R.2    Schulten, K.3
  • 15
    • 0001489180 scopus 로고
    • Systematic errors in free energy perturbation calculations due to a finite sample of configuration space. Sample-size hysteresis
    • Wood, R. H., Mühlbauer, W. C. F. and Thompson, P. T. (1991). "Systematic errors in free energy perturbation calculations due to a finite sample of configuration space. Sample-size hysteresis", J. Phys. Chem., 95, 6670.
    • (1991) J. Phys. Chem. , vol.95 , pp. 6670
    • Wood, R.H.1    Mühlbauer, W.C.F.2    Thompson, P.T.3
  • 16
    • 0242364982 scopus 로고    scopus 로고
    • Calculation of free energy differences from computer simulations of initial and final states
    • Hummer, G. and Szabo, A. (1996). "Calculation of free energy differences from computer simulations of initial and final states", J. Chem. Phys., 105, 2004.
    • (1996) J. Chem. Phys. , vol.105 , pp. 2004
    • Hummer, G.1    Szabo, A.2
  • 17
    • 33751143432 scopus 로고    scopus 로고
    • On the free energy of ionic hydration
    • Hummer, G., Pratt, L. R. and García, A. E. (1996). "On the free energy of ionic hydration", J. Phys. Chem., 100, 1206.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1206
    • Hummer, G.1    Pratt, L.R.2    García, A.E.3
  • 18
    • 0004840242 scopus 로고
    • On the exchange interaction in magnetic crystals
    • Opechowski, W. (1937). "On the exchange interaction in magnetic crystals", Phsika, 4, 181.
    • (1937) Phsika , vol.4 , pp. 181
    • Opechowski, W.1
  • 19
    • 0002678709 scopus 로고
    • Order and disorder in binary solid solutions
    • Kirkwood, J. G. (1938). "Order and disorder in binary solid solutions", J. Chem. Phys., 6, 70.
    • (1938) J. Chem. Phys. , vol.6 , pp. 70
    • Kirkwood, J.G.1
  • 20
    • 0000762204 scopus 로고    scopus 로고
    • Cumulant expansion of the free energy: Application to free energy derivatives and component analysis
    • Archontis, G. and Karplus, M. (1996). "Cumulant expansion of the free energy: Application to free energy derivatives and component analysis", J. Chem. Phys., 105, 11246.
    • (1996) J. Chem. Phys. , vol.105 , pp. 11246
    • Archontis, G.1    Karplus, M.2
  • 21
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu, H., 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., 100, 9485.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9485
    • Liu, H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 22
    • 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.
    • (1994) J. Chem. Phys. , vol.100 , pp. 577
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 23
    • 0001254876 scopus 로고
    • Microscopic formulation of Marcus theory of electron transfer
    • Zhou, H.-X. and Szabo, A. (1995). "Microscopic formulation of Marcus theory of electron transfer, J. Chem. Phys., 103, 3481.
    • (1995) J. Chem. Phys. , vol.103 , pp. 3481
    • Zhou, H.-X.1    Szabo, A.2
  • 24
    • 0035333627 scopus 로고    scopus 로고
    • Fast-growth thermodynamic integration: Error and efficiency analysis
    • in Press
    • Hummer, G. (2001). "Fast-growth thermodynamic integration: Error and efficiency analysis", J. Chem. Phys., in press.
    • (2001) J. Chem. Phys.
    • Hummer, G.1
  • 25
    • 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.
    • (1991) J. Phys. Chem. , vol.95 , pp. 9029
    • Hermans, J.1
  • 26
    • 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.
    • (1991) J. Phys. Chem. , vol.95 , pp. 4838
    • Wood, R.H.1
  • 27
    • 0004869739 scopus 로고
    • Formule d'interpolation de Lagrange
    • Edited by Picard, E
    • Hermite, C. (1878). "Formule d'interpolation de Lagrange, In: Œvres de Charles Hermite, Edited by Picard, E., 3, 432-443,
    • (1878) Œvres de Charles Hermite , vol.3 , pp. 432-443
    • Hermite, C.1
  • 28
    • 33746368349 scopus 로고
    • Gauthier-Villars, Paris
    • Gauthier-Villars, Paris (1912), originally published in: Journal de Crelle, 84, 70.
    • (1912) Journal de Crelle , vol.84 , pp. 70
  • 29
    • 36449009845 scopus 로고
    • Correlations and free energies in restricted primitive model descriptions of electrolytes
    • Hummer, G. and Soumpasis, D. M. (1993). "Correlations and free energies in restricted primitive model descriptions of electrolytes", J. Chem. Phys., 98, 58 1.
    • (1993) J. Chem. Phys. , vol.98 , pp. 581
    • Hummer, G.1    Soumpasis, D.M.2
  • 30
    • 0001029719 scopus 로고
    • On finite-size effects in computer simulations using the Ewald potential
    • Figueirido, F., Del Buono, G. S. and Levy, R. M. (1995). "On finite-size effects in computer simulations using the Ewald potential", J. Chem. Phys., 103, 6133.
    • (1995) J. Chem. Phys. , vol.103 , pp. 6133
    • Figueirido, F.1    Del Buono, G.S.2    Levy, R.M.3
  • 31
    • 0041824707 scopus 로고    scopus 로고
    • Ion sizes and finite-size corrections for ionic-solvation free energies
    • Hummer, G., Pratt, L. R. and Garía, A. E. (1997). "Ion sizes and finite-size corrections for ionic-solvation free energies", J. Chem. Phys., 107, 9275.
    • (1997) J. Chem. Phys. , vol.107 , pp. 9275
    • Hummer, G.1    Pratt, L.R.2    Garía, A.E.3
  • 32
    • 0000539134 scopus 로고    scopus 로고
    • Molecular theories and simulation of ions and polar molecules in water
    • Hummer, G., Pratt, L. R. and García, A. E. (1998). "Molecular theories and simulation of ions and polar molecules in water", J. Phys. Chem. A, 102, 7885.
    • (1998) J. Phys. Chem. A , vol.102 , pp. 7885
    • Hummer, G.1    Pratt, L.R.2    García, A.E.3
  • 33
    • 0000953090 scopus 로고    scopus 로고
    • On the effects of truncating the electrostatic interaction free energies of ion hydration
    • Kalko, S. G., Sese, G. and Padro, J. A. (1996). "On the effects of truncating the electrostatic interaction free energies of ion hydration", J. Chem. Phys., 104, 9578.
    • (1996) J. Chem. Phys. , vol.104 , pp. 9578
    • Kalko, S.G.1    Sese, G.2    Padro, J.A.3
  • 34
    • 0000078301 scopus 로고    scopus 로고
    • Effects of long-range electrostatic potential truncation on the free energy of ionic hydration
    • Ashbaugh, H. S. and Wood, R. H. (1997). "Effects of long-range electrostatic potential truncation on the free energy of ionic hydration", J. Chem. Phys., 106, 8135.
    • (1997) J. Chem. Phys. , vol.106 , pp. 8135
    • Ashbaugh, H.S.1    Wood, R.H.2
  • 35
    • 0031185669 scopus 로고    scopus 로고
    • On finite-size corrections to the free energy of ionic hydration
    • Figueirido, F., Del Buono, G. S. and Levy, R. M. (1997). "On finite-size corrections to the free energy of ionic hydration", J. Phys. Chem. B, 101, 5622.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5622
    • Figueirido, F.1    Del Buono, G.S.2    Levy, R.M.3
  • 36
    • 0028016368 scopus 로고
    • Ion pair potentials-of-mean-force in water
    • Pratt, L. R., Hummer, G. and García, A. E. (1994). "Ion pair potentials-of-mean-force in water", Biophys. Chem., 51, 147.
    • (1994) Biophys. Chem. , vol.51 , pp. 147
    • Pratt, L.R.1    Hummer, G.2    García, A.E.3
  • 37
    • 0022004980 scopus 로고
    • Electron transfer in chemistry and biology
    • Marcus, R. A. and Sutin, N. (1985). "Electron transfer in chemistry and biology", Biochim. Biophys. Acta, 811, 265.
    • (1985) Biochim. Biophys. Acta , vol.811 , pp. 265
    • Marcus, R.A.1    Sutin, N.2
  • 39
    • 0030774472 scopus 로고    scopus 로고
    • Multistate Gaussian model for electrostatic solvation free energies
    • Hummer, G., Pratt, L. R. and García, A. E. (1997). "Multistate Gaussian model for electrostatic solvation free energies", J. Am. Chem. Soc., 119, 8523.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 8523
    • Hummer, G.1    Pratt, L.R.2    García, A.E.3
  • 40
    • 0001487459 scopus 로고    scopus 로고
    • Free energy of hydration of a molecular ionic solute tetramethylammonium ion
    • Garde, S., Hummer, G. and Paulaitis, M. E. (1998). "Free energy of hydration of a molecular ionic solute tetramethylammonium ion", J. Chem. Phys., 108, 1552.
    • (1998) J. Chem. Phys. , vol.108 , pp. 1552
    • Garde, S.1    Hummer, G.2    Paulaitis, M.E.3
  • 41
    • 33749637456 scopus 로고
    • Free energy calculations of ion hydration: An analysis of the Born model in terms of microscopic simulations
    • Jayaram, B., Fine, R., Sharp, K. and Honig, B. (1989). "Free energy calculations of ion hydration: An analysis of the Born model in terms of microscopic simulations", J. Phys. Chem., 93, 4320.
    • (1989) J. Phys. Chem. , vol.93 , pp. 4320
    • Jayaram, B.1    Fine, R.2    Sharp, K.3    Honig, B.4
  • 42
    • 5544264558 scopus 로고
    • Gaussian fluctuation formula for electrostatic free energy changes in solution
    • Levy, R. M., Belhadj, M. and Kitchen, D. B. (1991). "Gaussian fluctuation formula for electrostatic free energy changes in solution", J. Chem. Phys., 95, 3627.
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 43
    • 0032233055 scopus 로고    scopus 로고
    • Computer simulations with explicit solvent. Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects
    • Levy, R. M. and Gallicchio, E. (1998). "Computer simulations with explicit solvent. Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects", Ann. Rev. Phys. Chem., 49, 531.
    • (1998) Ann. Rev. Phys. Chem. , vol.49 , pp. 531
    • Levy, R.M.1    Gallicchio, E.2
  • 44
    • 33845282688 scopus 로고
    • Microscopic examination of free energy relationships for electron transfer in polar solvents
    • Hwang, J. K. and Warshel, A. (1987). "Microscopic examination of free energy relationships for electron transfer in polar solvents", J. Am. Chem. Soc., 109, 715.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 715
    • Hwang, J.K.1    Warshel, A.2
  • 45
    • 0026596911 scopus 로고
    • Calculations of antibody antigen interactions. Microscopic and semimicroscopic evaluation of the free energies of binding of phosphorylcholine analogs to mcpc603
    • Lee, F. S., Chu, Z. T., Bolger, M. B. and Warshel, A. (1992). "Calculations of antibody antigen interactions. Microscopic and semimicroscopic evaluation of the free energies of binding of phosphorylcholine analogs to mcpc603", Protein Engin., 5, 215.
    • (1992) Protein Engin. , vol.5 , pp. 215
    • Lee, F.S.1    Chu, Z.T.2    Bolger, M.B.3    Warshel, A.4
  • 46
    • 0242677212 scopus 로고
    • Calculation of electrostatic free energy differences with a time-saving approximate method
    • King, G. and Barford, R. A. (1993). "Calculation of electrostatic free energy differences with a time-saving approximate method", J. Phys. Chem., 97, 8798.
    • (1993) J. Phys. Chem. , vol.97 , pp. 8798
    • King, G.1    Barford, R.A.2
  • 47
    • 0344796204 scopus 로고
    • Ion water interaction potentials derived from free energy perturbation simulations
    • Åqvist, J. (1990). "Ion water interaction potentials derived from free energy perturbation simulations", J. Phys. Chem., 94, 8021.
    • (1990) J. Phys. Chem. , vol.94 , pp. 8021
    • Åqvist, J.1
  • 48
    • 0031559501 scopus 로고    scopus 로고
    • From hydrophobic to hydrophilic hydration: A simulation study of solvation entropy and free energy of simple solutes
    • Lynden-Bell, R. M. and Rasaiah, J. C. (1997). "From hydrophobic to hydrophilic hydration: A simulation study of solvation entropy and free energy of simple solutes", J. Chem. Phys., 107, 1981.
    • (1997) J. Chem. Phys. , vol.107 , pp. 1981
    • Lynden-Bell, R.M.1    Rasaiah, J.C.2
  • 49
    • 0001458825 scopus 로고
    • The aqueous solvation of water: A comparison of continuum methods with molecular dynamics
    • Rick, S. W. and Berne, B. J. (1994). "The aqueous solvation of water: A comparison of continuum methods with molecular dynamics", J. Am. Chem. Soc., 116, 3949.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 3949
    • Rick, S.W.1    Berne, B.J.2
  • 51
    • 0001286784 scopus 로고    scopus 로고
    • Reply to comment on 'Electrostatic potentials and free energies of solvation of polar and charged molecules
    • Hummer, G., Pratt, L. R., García, A. E., Garde, S., Berne, B. J. and Rick, S. W. (1998). "Reply to comment on 'Electrostatic potentials and free energies of solvation of polar and charged molecules'", J. Phys. Chem. B, 102, 3841.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3841
    • Hummer, G.1    Pratt, L.R.2    García, A.E.3    Garde, S.4    Berne, B.J.5    Rick, S.W.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.