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Volumn 227, Issue 2, 2007, Pages 1246-1266

Extending the fast multipole method for charges inside a dielectric sphere in an ionic solvent: High-order image approximations for reaction fields

Author keywords

Electrostatic interaction; Fast multipole method; Hybrid solvent model; Ionic solvent; Method of images; Reaction field

Indexed keywords

ELECTROSTATICS; SOLVENTS;

EID: 36148998074     PISSN: 00219991     EISSN: 10902716     Source Type: Journal    
DOI: 10.1016/j.jcp.2007.09.001     Document Type: Article
Times cited : (21)

References (47)
  • 1
    • 33645981305 scopus 로고    scopus 로고
    • Electrostatics calculations: latest methodological advances
    • Koehl P. Electrostatics calculations: latest methodological advances. Curr. Opin. Struct. Biol. 16 (2006) 142-151
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 142-151
    • Koehl, P.1
  • 2
    • 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. Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu. Rev. Phys. Chem. 49 (1998) 531-567
    • (1998) Annu. Rev. Phys. Chem. , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 3
    • 0033024177 scopus 로고    scopus 로고
    • Molecular dynamics simulation of biomolecules: long-range electrostatic effects
    • Sagui C., and Darden T.A. Molecular dynamics simulation of biomolecules: long-range electrostatic effects. Annu. Rev. Biophys. Biomol. Struct. 28 (1999) 155-179
    • (1999) Annu. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 155-179
    • Sagui, C.1    Darden, T.A.2
  • 4
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • Feig M., and Brooks III C.L. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14 (2004) 217-224
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 5
    • 17044392602 scopus 로고    scopus 로고
    • Improving implicit solvent simulations: a Poisson-centric view
    • Baker N.A. Improving implicit solvent simulations: a Poisson-centric view. Curr. Opin. Struct. Biol. 15 (2005) 137-143
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 137-143
    • Baker, N.A.1
  • 6
    • 85189850140 scopus 로고    scopus 로고
    • A. Okur, C. Simmerling, Hybrid explicit/implicit solvation methods, in: D. Spellmeyer (Ed.), Annu. Rep. Comput. Chem., vol. 2, 2006 (Chapter 6).
  • 7
    • 9244224092 scopus 로고    scopus 로고
    • An efficient hybrid explicit/implicit solvent method for biomolecular simulations
    • Lee M.S., Salsbury Jr. F.R., and Olson M.A. An efficient hybrid explicit/implicit solvent method for biomolecular simulations. J. Comput. Chem. 25 (2004) 1967-1978
    • (2004) J. Comput. Chem. , vol.25 , pp. 1967-1978
    • Lee, M.S.1    Salsbury Jr., F.R.2    Olson, M.A.3
  • 8
    • 15744363770 scopus 로고    scopus 로고
    • Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method
    • Lee M.S., and Olson M.A. Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method. J. Phys. Chem. B 109 (2005) 5223-5236
    • (2005) J. Phys. Chem. B , vol.109 , pp. 5223-5236
    • Lee, M.S.1    Olson, M.A.2
  • 9
    • 36749119973 scopus 로고
    • Deformable stochastic boundaries in molecular-dynamics
    • Brooks III C.L., and Karplus M. Deformable stochastic boundaries in molecular-dynamics. J. Chem. Phys. 79 (1983) 6312-6325
    • (1983) J. Chem. Phys. , vol.79 , pp. 6312-6325
    • Brooks III, C.L.1    Karplus, M.2
  • 10
    • 0022068152 scopus 로고
    • Active-site dynamics in protein molecules - a stochastic boundary molecular-dynamics approach
    • Brooks III C.L., Brunger A., and Karplus M. Active-site dynamics in protein molecules - a stochastic boundary molecular-dynamics approach. Biopolymers 24 (1985) 843-865
    • (1985) Biopolymers , vol.24 , pp. 843-865
    • Brooks III, C.L.1    Brunger, A.2    Karplus, M.3
  • 11
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • King G., and Warshel A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91 (1989) 3647-3661
    • (1989) J. Chem. Phys. , vol.91 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 12
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system - Solvent boundary potential for computer simulations
    • Belgov D., and Roux B. Finite representation of an infinite bulk system - Solvent boundary potential for computer simulations. J. Chem. Phys. 100 (1994) 9050-9063
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Belgov, D.1    Roux, B.2
  • 13
    • 0001158363 scopus 로고
    • Monte-Carlo studies of dielectric properties of water-like models
    • Barker J.A., and Watts R.O. Monte-Carlo studies of dielectric properties of water-like models. Mol. Phys. 26 (1973) 789-792
    • (1973) Mol. Phys. , vol.26 , pp. 789-792
    • Barker, J.A.1    Watts, R.O.2
  • 14
    • 0008843911 scopus 로고
    • Reaction field, screening, and long-range interactions in simulations of ionic and dipolar systems
    • Barker J.A. Reaction field, screening, and long-range interactions in simulations of ionic and dipolar systems. Mol. Phys. 83 (1994) 1057-1064
    • (1994) Mol. Phys. , vol.83 , pp. 1057-1064
    • Barker, J.A.1
  • 15
    • 4544369164 scopus 로고
    • Generalized reaction field method for molecular dynamics simulations
    • Tironi I.G., Sperb R., Smith P.E., and van Gunsteren W.F. Generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 102 (1995) 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
  • 16
    • 20644431615 scopus 로고
    • Theory of solutions of molecules containing widely separated charges with special applications to awitterions
    • Kirkwood J.G. Theory of solutions of molecules containing widely separated charges with special applications to awitterions. J. Chem. Phys. 2 (1934) 351-361
    • (1934) J. Chem. Phys. , vol.2 , pp. 351-361
    • Kirkwood, J.G.1
  • 17
    • 84947145359 scopus 로고
    • Image approximation to the reaction field
    • Friedman H.L. Image approximation to the reaction field. Mol. Phys. 29 (1975) 1533-1543
    • (1975) Mol. Phys. , vol.29 , pp. 1533-1543
    • Friedman, H.L.1
  • 18
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R., and Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235 (1994) 983-1002
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 19
    • 33947099467 scopus 로고    scopus 로고
    • Extending the fast multipole method to charges inside or outside a dielectric sphere
    • Cai W., Deng S., and Jacobs D. Extending the fast multipole method to charges inside or outside a dielectric sphere. J. Comput. Phys. 223 (2007) 846-864
    • (2007) J. Comput. Phys. , vol.223 , pp. 846-864
    • Cai, W.1    Deng, S.2    Jacobs, D.3
  • 20
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
    • Warwicker J., and Watson H.C. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J. Mol. Biol. 157 (1982) 671-679
    • (1982) J. Mol. Biol. , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.2
  • 21
    • 1642464809 scopus 로고    scopus 로고
    • Poisson-Boltzmann methods for biomolecular electrostatics
    • Baker N.A. Poisson-Boltzmann methods for biomolecular electrostatics. Methods Enzymol 383 (2004) 94-118
    • (2004) Methods Enzymol , vol.383 , pp. 94-118
    • Baker, N.A.1
  • 22
    • 0036873086 scopus 로고    scopus 로고
    • The Poisson-Boltzmann equation for biomolecular electrostatics
    • Fogolari F., Brigo A., and Molinari H. The Poisson-Boltzmann equation for biomolecular electrostatics. J. Mol. Biol. 15 (2002) 377-392
    • (2002) J. Mol. Biol. , vol.15 , pp. 377-392
    • Fogolari, F.1    Brigo, A.2    Molinari, H.3
  • 23
    • 0037328258 scopus 로고    scopus 로고
    • Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution
    • Bordner A.J., and Huber G.A. Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution. J. Comput. Chem. 24 (2003) 353-367
    • (2003) J. Comput. Chem. , vol.24 , pp. 353-367
    • Bordner, A.J.1    Huber, G.A.2
  • 25
    • 33947468892 scopus 로고
    • Theory of protein titration curves. I. General equations for impenetrable spheres
    • Tanford C., and Kirkwood J.G. Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79 (1957) 5333-5339
    • (1957) J. Am. Chem. Soc. , vol.79 , pp. 5333-5339
    • Tanford, C.1    Kirkwood, J.G.2
  • 26
    • 0000652941 scopus 로고
    • Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations
    • Alper H., and Levy R.M. Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations. J. Chem. Phys. 99 (1993) 9847-9852
    • (1993) J. Chem. Phys. , vol.99 , pp. 9847-9852
    • Alper, H.1    Levy, R.M.2
  • 27
    • 36148949369 scopus 로고    scopus 로고
    • Discrete image approximations of ionic solvent induced reaction field to charges
    • Deng S., and Cai W. Discrete image approximations of ionic solvent induced reaction field to charges. Commun. Comput. Phys. 2 (2007) 1007-1026
    • (2007) Commun. Comput. Phys. , vol.2 , pp. 1007-1026
    • Deng, S.1    Cai, W.2
  • 32
    • 0026678802 scopus 로고
    • Electrostatic image theory for the dielectric sphere
    • Lindell I.V. Electrostatic image theory for the dielectric sphere. Radio Sci. 27 (1992) 1-8
    • (1992) Radio Sci. , vol.27 , pp. 1-8
    • Lindell, I.V.1
  • 33
    • 0029275990 scopus 로고
    • Charge images in a dielectric sphere
    • Norris W.T. Charge images in a dielectric sphere. IEE Proc.-Sci. Meas. Technol. 142 (1995) 142-150
    • (1995) IEE Proc.-Sci. Meas. Technol. , vol.142 , pp. 142-150
    • Norris, W.T.1
  • 36
    • 0028388229 scopus 로고
    • Algorithm 726; ORTHPOL - a package of routines for generating orthogonal polynomials and Gauss-type quadrature rules
    • Gautschi W. Algorithm 726; ORTHPOL - a package of routines for generating orthogonal polynomials and Gauss-type quadrature rules. ACM Trans. Math. Softw. 20 (1994) 21-62
    • (1994) ACM Trans. Math. Softw. , vol.20 , pp. 21-62
    • Gautschi, W.1
  • 37
    • 0002439750 scopus 로고
    • An efficient program for many-body simulation
    • Appel A. An efficient program for many-body simulation. SIAM J. Sci. Stat. Comput. 6 (1985) 85-103
    • (1985) SIAM J. Sci. Stat. Comput. , vol.6 , pp. 85-103
    • Appel, A.1
  • 38
    • 33846349887 scopus 로고
    • A hierarchical O(Nlog N) force-calculation algorithm
    • Barnes J., and Hut P. A hierarchical O(Nlog N) force-calculation algorithm. Nature 324 (1986) 446-449
    • (1986) Nature , vol.324 , pp. 446-449
    • Barnes, J.1    Hut, P.2
  • 39
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An Nlog N method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald: An Nlog N method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 40
  • 41
    • 0000396658 scopus 로고
    • A fast algorithm for particle simulations
    • Greengard L., and Rokhlin V. A fast algorithm for particle simulations. J. Comput. Phys. 73 (1987) 325-348
    • (1987) J. Comput. Phys. , vol.73 , pp. 325-348
    • Greengard, L.1    Rokhlin, V.2
  • 43
    • 85011484616 scopus 로고    scopus 로고
    • A new version of the fast multipole method for the Laplace equation in three dimensions
    • Greengard L., and Roklin V. A new version of the fast multipole method for the Laplace equation in three dimensions. Acta Numer. 6 (1997) 229-269
    • (1997) Acta Numer. , vol.6 , pp. 229-269
    • Greengard, L.1    Roklin, V.2
  • 44
    • 0000362580 scopus 로고    scopus 로고
    • A fast adaptive multipole algorithm in three dimensions
    • Cheng H., Greengard L., and Roklin V. A fast adaptive multipole algorithm in three dimensions. J. Comput. Phys. 155 (1999) 468-498
    • (1999) J. Comput. Phys. , vol.155 , pp. 468-498
    • Cheng, H.1    Greengard, L.2    Roklin, V.3
  • 45
    • 0037055750 scopus 로고    scopus 로고
    • A new version of the fast multipole method for screened Coulomb interactions in three dimensions
    • Greengard L.F., and Huang J. A new version of the fast multipole method for screened Coulomb interactions in three dimensions. J. Comput. Phys. 180 (2002) 642-658
    • (2002) J. Comput. Phys. , vol.180 , pp. 642-658
    • Greengard, L.F.1    Huang, J.2
  • 46
    • 33845868249 scopus 로고    scopus 로고
    • Order N algorithm for computation of electrostatic interactions in biomolecular systems
    • Lu B., Cheng X., Huang J., and McCammon J.A. Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc. Natl. Acad. Sci. USA. 103 (2006) 19314-19319
    • (2006) Proc. Natl. Acad. Sci. USA. , vol.103 , pp. 19314-19319
    • Lu, B.1    Cheng, X.2    Huang, J.3    McCammon, J.A.4
  • 47
    • 0026255002 scopus 로고
    • Fastcap: A multipole accelerated 3D capacitance extraction program
    • Nabors K., and White J.K. Fastcap: A multipole accelerated 3D capacitance extraction program. IEEE Trans. CAD 10 (1991) 1447-1459
    • (1991) IEEE Trans. CAD , vol.10 , pp. 1447-1459
    • Nabors, K.1    White, J.K.2


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