메뉴 건너뛰기




Volumn 28, Issue , 1999, Pages 155-179

Molecular dynamics simulations of biomolecules: Long-range electrostatic effects

Author keywords

Ewald summation; Fast multipole; Free energies; Particle mesh Ewald; Periodic boundary conditions

Indexed keywords

ARTICLE; COMPUTER SIMULATION; ELECTRICITY; INTERMETHOD COMPARISON; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; TECHNIQUE;

EID: 0033024177     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.28.1.155     Document Type: Article
Times cited : (543)

References (73)
  • 1
    • 0030904524 scopus 로고    scopus 로고
    • Novel methods of sampling phase space in the simulation of biological systems
    • 1. Berne BJ, Straub JE. 1997. Novel methods of sampling phase space in the simulation of biological systems. Curr. Opin. Struct. Biol. 7:181-89
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 181-189
    • Berne, B.J.1    Straub, J.E.2
  • 2
    • 0031123703 scopus 로고    scopus 로고
    • From silicon to RNA: The coming of age of ab initio molecular dynamics
    • 2. Parrinello M. 1997. From silicon to RNA: the coming of age of ab initio molecular dynamics. Solid State Commun. 102:107-20
    • (1997) Solid State Commun. , vol.102 , pp. 107-120
    • Parrinello, M.1
  • 3
    • 0000054413 scopus 로고    scopus 로고
    • A real-space multigrid-based approach to large-scale electronic structure calculations
    • 3. Briggs EL, Sullivan DJ, Bernhole J. 1996. A real-space multigrid-based approach to large-scale electronic structure calculations. Phys. Rev. B 54:14362
    • (1996) Phys. Rev. B , vol.54 , pp. 14362
    • Briggs, E.L.1    Sullivan, D.J.2    Bernhole, J.3
  • 5
    • 0030371152 scopus 로고    scopus 로고
    • 'Covalent' effects in 'ionic' systems
    • 5. Madden PA, Wilson M. 1996. 'Covalent' effects in 'ionic' systems. Chem. Soc. Rev. 25:339-50
    • (1996) Chem. Soc. Rev. , vol.25 , pp. 339-350
    • Madden, P.A.1    Wilson, M.2
  • 6
    • 85047697575 scopus 로고    scopus 로고
    • Novel simulation model for many-body multipole dispersion interactions
    • 6. van der Hoef MA, Madden PA. 1998. Novel simulation model for many-body multipole dispersion interactions. Mol. Phys. 94:417-33
    • (1998) Mol. Phys. , vol.94 , pp. 417-433
    • Van Der Hoef, M.A.1    Madden, P.A.2
  • 8
    • 0002592235 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids
    • New York: Wiley & Sons. In press
    • 8. Auffinger P, Westhof E. 1999. Molecular dynamics simulations of nucleic acids. In Encyclopedia of Computational Chemistry. New York: Wiley & Sons. In press
    • (1999) Encyclopedia of Computational Chemistry
    • Auffinger, P.1    Westhof, E.2
  • 10
    • 0026755515 scopus 로고
    • Cutoff size does strongly influence molecular dynamics results on solvated polypeptides
    • 10. Schreiber H, Steinhauser O. 1992. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 31:5856-60
    • (1992) Biochemistry , vol.31 , pp. 5856-5860
    • Schreiber, H.1    Steinhauser, O.2
  • 11
    • 0029110156 scopus 로고    scopus 로고
    • Towards the accurate modeling of DNA: The importance of long-range electrostatics
    • 11. York DM, Yang W, Darden T, Pedersen LG. Towards the accurate modeling of DNA: the importance of long-range electrostatics. J. Am. Chem. Soc. 117:5001-2
    • J. Am. Chem. Soc. , vol.117 , pp. 5001-5002
    • York, D.M.1    Yang, W.2    Darden, T.3    Pedersen, L.G.4
  • 12
    • 84986534166 scopus 로고
    • New spherical cutoff methods for long-range forces in macromolecular simulation
    • 12. Steinbach PJ, Brooks BR. 1994. New spherical cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15:667-83
    • (1994) J. Comp. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.R.2
  • 13
    • 0030782840 scopus 로고    scopus 로고
    • Influence of magnesium ions on duplex DNA: Structural, dynamic, and solvation properties
    • 13. MacKerrell AD. 1997. Influence of magnesium ions on duplex DNA: structural, dynamic, and solvation properties. J. Phys. Chem. B 101:646-50
    • (1997) J. Phys. Chem. B , vol.101 , pp. 646-650
    • MacKerrell, A.D.1
  • 14
    • 0000951252 scopus 로고    scopus 로고
    • Effect of electrostatic force truncation on interfacial and transport properties of water
    • 14. Feller SE, Pastor RW, Rojnuckarin A, Bogusz S, Brooks BR. 1996. Effect of electrostatic force truncation on interfacial and transport properties of water. J. Phys. Chem. 100:17011-20
    • (1996) J. Phys. Chem. , vol.100 , pp. 17011-17020
    • Feller, S.E.1    Pastor, R.W.2    Rojnuckarin, A.3    Bogusz, S.4    Brooks, B.R.5
  • 15
    • 0032054517 scopus 로고    scopus 로고
    • Electrostatic effects in macromolecules: Fundamental concepts and practical modeling
    • 15. Warshel A, Papazyan A. 1998. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. Curr. Opin. Struct. Biol. 8:211-17
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 211-217
    • Warshel, A.1    Papazyan, A.2
  • 16
    • 0001913113 scopus 로고
    • Point multipoles in the Ewald summation
    • 16. Smith W. 1982. Point multipoles in the Ewald summation. CCP5 Inf. Q. 4:13-25
    • (1982) CCP5 Inf. Q. , vol.4 , pp. 13-25
    • Smith, W.1
  • 17
    • 84977266737 scopus 로고
    • Die Berechnung optischer und elektrostatischer Gitterpotentiale
    • 17. Ewald P. 1921. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 64:253-87
    • (1921) Ann. Phys. , vol.64 , pp. 253-287
    • Ewald, P.1
  • 19
    • 0030172529 scopus 로고    scopus 로고
    • Comments on PPPM, FMM, and the Ewald method for large periodic Coulombic systems
    • 19. Pollock E, Glosli J. 1996. Comments on PPPM, FMM, and the Ewald method for large periodic Coulombic systems. Camp. Phys. Comm. 95:93-110
    • (1996) Camp. Phys. Comm. , vol.95 , pp. 93-110
    • Pollock, E.1    Glosli, J.2
  • 20
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log (N) method for Ewald sums in large systems
    • 20. Darden TA, York DM, Pedersen LG. 1993. Particle mesh Ewald: an N log (N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-92
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.M.2    Pedersen, L.G.3
  • 22
    • 0000316648 scopus 로고    scopus 로고
    • Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics
    • 22. Bishop T, Skeel R, Schulten K. 1997. Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics. J. Comp. Chem. 18:1785-91
    • (1997) J. Comp. Chem. , vol.18 , pp. 1785-1791
    • Bishop, T.1    Skeel, R.2    Schulten, K.3
  • 23
    • 0000396658 scopus 로고
    • A fast algorithm for particle simultations
    • 23. Greengard L, Rokhlin V. 1987. A fast algorithm for particle simultations. J. Camp. Phys. 73:325-48
    • (1987) J. Camp. Phys. , vol.73 , pp. 325-348
    • Greengard, L.1    Rokhlin, V.2
  • 25
    • 0031168817 scopus 로고    scopus 로고
    • Large scale simulation of macro-molecules in solution: Combining the periodic fast multipole method with multiple time step integrators
    • 25. Figuerido F, Levy R, Zhou R, Berne B. 1997. Large scale simulation of macro-molecules in solution: combining the periodic fast multipole method with multiple time step integrators. J. Chem. Phys. 106:9835-49
    • (1997) J. Chem. Phys. , vol.106 , pp. 9835-9849
    • Figuerido, F.1    Levy, R.2    Zhou, R.3    Berne, B.4
  • 28
    • 84926811618 scopus 로고
    • Constant pressure molecular dynamics for molecular systems
    • 28. Nose S, Klein M. 1983. Constant pressure molecular dynamics for molecular systems. Mol. Phys. 50:1055-76
    • (1983) Mol. Phys. , vol.50 , pp. 1055-1076
    • Nose, S.1    Klein, M.2
  • 29
    • 0001786236 scopus 로고
    • Simulation of electrostatic systems in periodic boundary conditions I: Lattice sums and dielectric constants
    • 29. DeLeeuw SW, Perram JW, Smith ER. 1980. Simulation of electrostatic systems in periodic boundary conditions I: lattice sums and dielectric constants. Proc. R. Soc. Lond. A373:27-56
    • (1980) Proc. R. Soc. Lond. , vol.A373 , pp. 27-56
    • DeLeeuw, S.W.1    Perram, J.W.2    Smith, E.R.3
  • 30
    • 21844519309 scopus 로고
    • Calculating the pressure in simulations using periodic boundary conditions
    • 30. Smith ER. 1994. Calculating the pressure in simulations using periodic boundary conditions. J. Stat. Phys. 77:449-72
    • (1994) J. Stat. Phys. , vol.77 , pp. 449-472
    • Smith, E.R.1
  • 31
    • 36449001805 scopus 로고
    • Comments on the numerical simulations of electrolytes in periodic boundary conditions
    • 31. Caillol JP. 1994. Comments on the numerical simulations of electrolytes in periodic boundary conditions. J. Chem. Phys. 101:6080-90
    • (1994) J. Chem. Phys. , vol.101 , pp. 6080-6090
    • Caillol, J.P.1
  • 33
    • 0001148922 scopus 로고    scopus 로고
    • Presumed versus real artifacts of the Ewald summation technique: The importance of dielectric boundary conditions
    • 33. Boresch S, Steinhauser O. 1997. Presumed versus real artifacts of the Ewald summation technique: the importance of dielectric boundary conditions. Ber. Bunsenges. Phys. Chem. 101:1019-29
    • (1997) Ber. Bunsenges. Phys. Chem. , vol.101 , pp. 1019-1029
    • Boresch, S.1    Steinhauser, O.2
  • 34
    • 0347010920 scopus 로고
    • A new formulation of the Hartree-Fock-Roothan method for structure calculations on crystals
    • 34. Hammes-Schiffer S, Andersen H. 1994. A new formulation of the Hartree-Fock-Roothan method for structure calculations on crystals. J. Chem. Phys. 101:375-93
    • (1994) J. Chem. Phys. , vol.101 , pp. 375-393
    • Hammes-Schiffer, S.1    Andersen, H.2
  • 35
    • 33751046558 scopus 로고
    • An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles
    • 35. Perram JW, Petersen HG, DeLeeuw SW. 1988. An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles. Mol. Phys. 65:875-93
    • (1988) Mol. Phys. , vol.65 , pp. 875-893
    • Perram, J.W.1    Petersen, H.G.2    DeLeeuw, S.W.3
  • 36
    • 0000064361 scopus 로고
    • An optimized method for treating long-range potentials
    • 36. Natoli V, Ceperley DM. 1995. An optimized method for treating long-range potentials. J. Comp. Phys. 117:171-78
    • (1995) J. Comp. Phys. , vol.117 , pp. 171-178
    • Natoli, V.1    Ceperley, D.M.2
  • 37
    • 0013603851 scopus 로고    scopus 로고
    • Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time scale algorithm
    • 37. Procachi P, Marchi M. 1996. Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time scale algorithm. J. Chem. Phys.
    • (1996) J. Chem. Phys.
    • Procachi, P.1    Marchi, M.2
  • 38
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • 38. Tuckerman ME, Berne BJ, Martyna GJ. 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
  • 39
    • 0030163950 scopus 로고    scopus 로고
    • Ewald sum techniques in perspective: A survey
    • 39. Toukmaji A, Board JA. 1996. Ewald sum techniques in perspective: a survey. Comp. Phys. Comm. 95:78-92
    • (1996) Comp. Phys. Comm. , vol.95 , pp. 78-92
    • Toukmaji, A.1    Board, J.A.2
  • 40
    • 0030764082 scopus 로고    scopus 로고
    • Long-range electrostatic effects in biomolecular simulations
    • 40. Darden T, Toukmaji A, Pedersen L. 1997. Long-range electrostatic effects in biomolecular simulations. J. Chem. Phys. 94:1346-64
    • (1997) J. Chem. Phys. , vol.94 , pp. 1346-1364
    • Darden, T.1    Toukmaji, A.2    Pedersen, L.3
  • 41
    • 22244433235 scopus 로고    scopus 로고
    • How to mesh up Ewald sums: A theoretical and numerical comparison of various particle mesh routines
    • 41. Deserno M, Holm C. 1998. How to mesh up Ewald sums: a theoretical and numerical comparison of various particle mesh routines. J. Chem. Phys. 109:7678-93
    • (1998) J. Chem. Phys. , vol.109 , pp. 7678-7693
    • Deserno, M.1    Holm, C.2
  • 42
    • 0000091410 scopus 로고    scopus 로고
    • How to mesh up Ewald sums II: An accurate error estimate for the particle-particle particle-mesh algorithm
    • 41a. Deserno M, Holm C. 1998. How to mesh up Ewald sums II: An accurate error estimate for the particle-particle particle-mesh algorithm. J. Chem. Phys. 109:7694-701
    • (1998) J. Chem. Phys. , vol.109 , pp. 7694-7701
    • Deserno, M.1    Holm, C.2
  • 43
    • 21844487185 scopus 로고
    • Particle-mesh methods on the connection machine
    • 42. Ferrell R, Bertschinger E. 1994. Particle-mesh methods on the connection machine. J. Mod. Phys. 5:933-56
    • (1994) J. Mod. Phys. , vol.5 , pp. 933-956
    • Ferrell, R.1    Bertschinger, E.2
  • 44
    • 0002553781 scopus 로고
    • Molecular-dynamics simulations of Coulomb systems in two and three dimensions
    • ed. G Ciccotti, WG Hoover. Amsterdam: North Holland
    • 43. Hansen J. 1986. Molecular-dynamics simulations of Coulomb systems in two and three dimensions. In Molecular Dynamics Simulation of Statistical-Mechanical Systems, ed. G Ciccotti, WG Hoover. Amsterdam: North Holland
    • (1986) Molecular Dynamics Simulation of Statistical-mechanical Systems
    • Hansen, J.1
  • 46
    • 0013605528 scopus 로고
    • Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions
    • 45. Shimada J, Kaneko H, Takada T. 1993. Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions. J. Comp. Chem. 14:867-78
    • (1993) J. Comp. Chem. , vol.14 , pp. 867-878
    • Shimada, J.1    Kaneko, H.2    Takada, T.3
  • 47
    • 0002997010 scopus 로고
    • A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic systems
    • 46. Luty BA, Davis ME, Tironi IG, van Gunsteren WF. 1994. A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic systems. Mol. Simul. 14:11-20
    • (1994) Mol. Simul. , vol.14 , pp. 11-20
    • Luty, B.A.1    Davis, M.E.2    Tironi, I.G.3    Van Gunsteren, W.F.4
  • 48
    • 33744994616 scopus 로고
    • The Fast Fourier Poisson (FFP) method for calculating Ewald sums
    • 47. York D, Yang W. 1994. The Fast Fourier Poisson (FFP) method for calculating Ewald sums. J. Chem. Phys. 101:3298
    • (1994) J. Chem. Phys. , vol.101 , pp. 3298
    • York, D.1    Yang, W.2
  • 49
    • 0028021598 scopus 로고
    • Fast algorithms for classical physics
    • 48. Greengard LF. 1994. Fast algorithms for classical physics. Science 265:909-14
    • (1994) Science , vol.265 , pp. 909-914
    • Greengard, L.F.1
  • 50
    • 85011484616 scopus 로고    scopus 로고
    • A new version of the fast multipole method for the Laplace equation in three dimensions
    • 49. Greengard L, Rokhlin V. 1997. A new version of the fast multipole method for the Laplace equation in three dimensions. Acta Numer. 6:229-70
    • (1997) Acta Numer. , vol.6 , pp. 229-270
    • Greengard, L.1    Rokhlin, V.2
  • 52
    • 0002439750 scopus 로고
    • An efficient program for many-body simulations
    • 51. Appel AW. 1985. An efficient program for many-body simulations. SIAM J. Sci. Stat. Comput. 6:85-103
    • (1985) SIAM J. Sci. Stat. Comput. , vol.6 , pp. 85-103
    • Appel, A.W.1
  • 53
    • 33846349887 scopus 로고
    • A hierarchical O (N log N) force-calculation algorithm
    • 52. Barnes J, Hut P. 1986. A hierarchical O (N log N) force-calculation algorithm. Nature 324:446-49
    • (1986) Nature , vol.324 , pp. 446-449
    • Barnes, J.1    Hut, P.2
  • 54
    • 0000242569 scopus 로고
    • A comparison of algorithms for long-range interactions
    • 53. Esselink K. 1995. A comparison of algorithms for long-range interactions. Comp. Phys. Comm. 87:375-95
    • (1995) Comp. Phys. Comm. , vol.87 , pp. 375-395
    • Esselink, K.1
  • 55
    • 34249919671 scopus 로고
    • Implementing the fast multipole method in three dimensions
    • 54. Schmidt KE, Lee MA. 1991. Implementing the fast multipole method in three dimensions. J. Stat. Phys. 63:1223-35
    • (1991) J. Stat. Phys. , vol.63 , pp. 1223-1235
    • Schmidt, K.E.1    Lee, M.A.2
  • 56
    • 0030188166 scopus 로고    scopus 로고
    • A multipole-based method for efficient calculation of forces and potentials in macroscopic periodic assemblies of particles
    • 55. Lambert CG, Darden TA, Board JA. 1996. A multipole-based method for efficient calculation of forces and potentials in macroscopic periodic assemblies of particles. J. Comp. Phys. 126:274-85
    • (1996) J. Comp. Phys. , vol.126 , pp. 274-285
    • Lambert, C.G.1    Darden, T.A.2    Board, J.A.3
  • 57
    • 0031185669 scopus 로고    scopus 로고
    • On finite-sire corrections to the free energy of ionic hydration
    • 56. Figuerido H, Buono GD, Levy RM. 1997. On finite-sire corrections to the free energy of ionic hydration. J. Phys. Chem. B 101:5622-23
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5622-5623
    • Figuerido, H.1    Buono, G.D.2    Levy, R.M.3
  • 58
    • 0343881269 scopus 로고
    • Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA
    • 57. Fenley M, Olson W, Chua K, Boschitsch A. 1994. Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA. J. Comp. Chem. 17:976
    • (1994) J. Comp. Chem. , vol.17 , pp. 976
    • Fenley, M.1    Olson, W.2    Chua, K.3    Boschitsch, A.4
  • 59
    • 36449007976 scopus 로고
    • The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
    • 58. York DM, Darden TA, Pedersen LG. 1993. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys. 99:8345-48
    • (1993) J. Chem. Phys. , vol.99 , pp. 8345-8348
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3
  • 60
    • 0000112790 scopus 로고    scopus 로고
    • Ewald artifacts in liquid state molecular dynamics simulations
    • 59. Smith PE, Pettitt BM. 1996. Ewald artifacts in liquid state molecular dynamics simulations. J. Chem. Phys. 105:4289-93
    • (1996) J. Chem. Phys. , vol.105 , pp. 4289-4293
    • Smith, P.E.1    Pettitt, B.M.2
  • 61
    • 0001476142 scopus 로고    scopus 로고
    • On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution
    • 60. Smith PE, Pettitt BM. 1997. On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution. J. Phys. Chem. B 101:3886-90
    • (1997) J. Phys. Chem. B , vol.101 , pp. 3886-3890
    • Smith, P.E.1    Pettitt, B.M.2
  • 62
    • 0031587288 scopus 로고    scopus 로고
    • Kinetics of peptide folding: Computer simulations of STPFDV and peptide variants in water
    • 61. Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. 1997. Kinetics of peptide folding: computer simulations of STPFDV and peptide variants in water. J. Mol. Biol. 272:423-42
    • (1997) J. Mol. Biol. , vol.272 , pp. 423-442
    • Mohanty, D.1    Elber, R.2    Thirumalai, D.3    Beglov, D.4    Roux, B.5
  • 63
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
    • 62. Harvey SH, Tan RK, Cheatham TE III. 1998. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comp. Chem. 19:726-40
    • (1998) J. Comp. Chem. , vol.19 , pp. 726-740
    • Harvey, S.H.1    Tan, R.K.2    Cheatham T.E. III3
  • 64
    • 84986440341 scopus 로고
    • Settle: An analytical version of the shake and rattle algorithms for rigid water molecules
    • 63. Miyamoto S, Kollman P. 1992. Settle: an analytical version of the shake and rattle algorithms for rigid water molecules. J. Comp. Chem. 13:952-62
    • (1992) J. Comp. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.2
  • 65
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • 64. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE III, et al. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Comm. 91:1-41
    • (1995) Comp. Phys. Comm. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham T.E. III5
  • 66
    • 0032233055 scopus 로고    scopus 로고
    • Computer simulations with explicit solvent: Recent progress in the thermodynamic decomposition of free energies, and in modeling electrostatic effects
    • 65. Levy RM, Gallicchio E. 1998. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies, and in modeling electrostatic effects. Annu. Rev. Phys. Chem. 49:531-67
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 67
    • 33751143432 scopus 로고    scopus 로고
    • On the free energy of ionic hydration
    • 66. Hummer G, Pratt LR, Garcia AE. 1996. On the free energy of ionic hydration. J. Phys. Chem. 100:1206-15
    • (1996) J. Phys. Chem. , vol.100 , pp. 1206-1215
    • Hummer, G.1    Pratt, L.R.2    Garcia, A.E.3
  • 68
    • 0041824707 scopus 로고    scopus 로고
    • Ion sizes and finite-size corrections for ionic-solvation free energies
    • 67. Hummer G, Pratt LR, Garcia AE. 1997. Ion sizes and finite-size corrections for ionic-solvation free energies. J. Chem. Phys. 107:9275-77
    • (1997) J. Chem. Phys. , vol.107 , pp. 9275-9277
    • Hummer, G.1    Pratt, L.R.2    Garcia, A.E.3
  • 69
    • 0001457283 scopus 로고    scopus 로고
    • Continuum corrections to the polarization and thermodynamic properties of Ewald sum simulations for ions and ion pairs at infinite dilution
    • 68. Sakane S, Ashbaugh HS, Wood RH. 1998. Continuum corrections to the polarization and thermodynamic properties of Ewald sum simulations for ions and ion pairs at infinite dilution. J. Phys. Chem. B 102: 5673-82
    • (1998) J. Phys. Chem. B , vol.102 , pp. 5673-5682
    • Sakane, S.1    Ashbaugh, H.S.2    Wood, R.H.3
  • 70
    • 0344796204 scopus 로고
    • Ion-water interaction potentials derived from free energy perturbation simulations
    • 69. Aqvist J. 1990. Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94:8021-24
    • (1990) J. Phys. Chem. , vol.94 , pp. 8021-8024
    • Aqvist, J.1
  • 71
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • 70. King G, Warshel A. 1989. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91:3647-61
    • (1989) J. Chem. Phys. , vol.91 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 72
    • 0000642138 scopus 로고    scopus 로고
    • Ionic charging free energies: Spherical versus periodic boundary conditions
    • 71. Darden T, Pearlman D, Pedersen L. 1998. Ionic charging free energies: spherical versus periodic boundary conditions. J. Chem. Phys. 109:10921-35
    • (1998) J. Chem. Phys. , vol.109 , pp. 10921-10935
    • Darden, T.1    Pearlman, D.2    Pedersen, L.3
  • 73
    • 0030918284 scopus 로고    scopus 로고
    • Biomolecular dynamics at long timesteps: Bridging the timescale gap between simulation and experiment
    • 72. Schlick T, Barth E, Mandziuk M. 1997. Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experiment. Annu. Rev. Biophys. Biomol. Struct. 26:181-222
    • (1997) Annu. Rev. Biophys. Biomol. Struct. , vol.26 , pp. 181-222
    • Schlick, T.1    Barth, E.2    Mandziuk, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.