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Original Articles

A Modulated Bulk as a Fuzzy Boundary for the Simulation of Long-Ranged Inhomogeneous Systems

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Pages 313-329 | Received 01 Sep 1993, Accepted 01 Jul 1994, Published online: 23 Sep 2006

References

  • Allen , M. P. and Tildesley , D. J. 1987 . Computer Simulation of Liquids , Oxford : Clarendon Press .
  • Guldbrand , L. E. , Forester , T. R. and Lynden-Bell , R. M. 1989 . Distribution and dynamics of mobile ions systems of ordered B-DNA . Mol. Phys. , 67 : 473
  • Hirshfelder , J. O. , Curtiss , C. F. and Bird , R. B. 1954 . The molecular theory of gases and Liquids , New York : Wiley .
  • Marcus , R. A. 1955 . Calculation of thermodynamic properties of polyelectrolytes . J. Chem. Phys. , 23 : 1057
  • Murthy , C. S. , Bacquet , R. and Rossky , P. J. 1985 . Ionic distributions near polyelectrolytes. A comparison of theoretical approaches . J. Phys. Chem. , 89 : 701
  • Penfold , R. , Jönsson , B. and Nordholm , S. 1993 . Ion-ion correlations in polyelectrolyte solutions: hard sphere counterions . J. Phys. Chem. , 99 : 497
  • Valleau , J. P. and Gardner , A. A. 1987 . Water-like particles at surfaces. I. The uncharged, unpolarized surface . J. Chem. Phys. , 86 : 4162
  • Gordon , H. L. and Goldman , S. 1989 . The glassy wall boundary for simulations of inhomogeneous systems . Molecular Simulation , 3 : 315
  • Zhang , L. , Davis , H. T. and White , H. S. 1993 . Simulations of solvent effects on confined electrolytes . J. Chem. Phys. , 98 : 5793
  • Linse , P. and Halle , B. 1989 . Counterion N. M. R. in heterogeneous aqueous systems. A Molecular Dynamics simulation study of the electric field gradient . Mol. Phys. , 67 : 537
  • Reddy , M. R. , Rossky , P. J. and Murthy , C. S. 1987 . Counterion spin relaxation in DNA solutions: a stochastic dynamics simulation study . J. Phys. Chem. , 91 : 4293
  • Brooks , C. L. and Karplus , M. 1983 . Deformable stochastic boundaries in Molecular Dynamics . J. Chem. Phys. , 79 : 6321
  • King , G. and Warshel , A. 1989 . A surface constrained all-atom solvent model for effective simulations of polar solutions . J. Chem. Phys. , 91 : 3647
  • Juffer , A. H. and Berendsen , H. J. C. 1993 . Dynamic surface boundary conditions: a simple boundary model for molecular dynamics simulations . Mol. Phys. , 79 : 623
  • Mezei , M. 1993 . The case for keeping simulated clusters spherical . CCP5 Quarterly , 37 : 38
  • Clarke , J. H. R. , Smith , W. and Woodcock , L. V. 1986 . Short range effective potentials for ionic fluids . J. Chem. Phys. , 84 : 2290
  • Brooks , C. L. , Pettitt , B. M. and Karplus , M. 1985 . Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids . J. Chem. Phys. , 83 : 5897
  • Prevost , M. , van Belle , D. , Lippens , G. and Wodak , S. 1990 . Computer simulation of liquid water: treatment of long-range interactions . Mol. Phys. , 71 : 587
  • Mills , P. , Anderson , C. F. and Record , M. T. Jr. 1985 . Monte Carlo studies of counterion-DNA, interactions. Comparison of the radial distribution of counterions with predictions of other polyelectrolyte theories . J. Phys. Chem. , 89 : 3984
  • Vlachy , V. and Haymet , A. D. J. 1986 . A grand cononical Monte Carlo simulation study of polyelectrolyte solutions . J. Chem. Phys. , 84 : 5874
  • Adams , D. 1983 . Alternatives to the periodic cube in computer simulation . CCP5 Quarterly , 10 : 30
  • Smith , W. 1983 . The periodic boundary condition in non-cubic MD cells: Wigner–Seitz cells with reflection symmetry . CCP5 Quarterly , 10 : 37
  • Abascal , J. L. F. , Bresme , F. and Turq , P. 1994 . The influence of concentration and ionic strength on the cluster structure of highly charged electrolyte solutions . Mol. Phys. , 81 : 143
  • Bresme , F. and Abascal , J. L. F. 1993 . Pair connectedness functions and percolation in highly charged electrolyte solutions . J. Chem. Phys. , 99 : 9037
  • Gil Montoro , J. C. and Abascal , J. L. F. 1993 . The Voronoi polyhedra as tools for structure determination in simple disordered systems . J. Phys. Chem. , 97 : 4211
  • Gil Montoro , J. C. , Bresme , F. and Abascal , J. L. F. Ionic association in electrolyte solutions: a Voronoi polyhedra analysis . J. Chem. Phys. , (in press)
  • Smith , P. E. and Pettitt , B. M. 1991 . Peptides in ionic solutions: a comparison of the Ewald and switching function techniques . J. Chem. Phys. , 95 : 8430
  • Vorontsov-Velyaminov , P. N. and Lyubartsev , A. P. 1992 . Monte Carlo-self consistent field study of the symmetrical models of polyelectrolytes . Molecular Simulation , 9 : 285
  • Linse , P. 1990 . Accurate solution of a highly asymmetric electrolyte: Molecular Dynamics simulation and integral equation . J. Chem. Phys. , 93 : 1376
  • Rossky , P. J. , Dudowick , J. B. , Tembe , B. L. and Friedman , H. L. 1980 . Ionic association in model 2:2 electrolyte solutions . J. Chem. Phys. , 73 : 3372
  • York , D. M. , Darden , T. , Deerfield , D. II and Pedersen , L. G. 1992 . The interaction of Na(I), Ca(II), and Mg(II) metal ions with duplex DNA: a theoretical modeling study . Inter. J. of Quantum Chem: Quantum Biology Symposium , 19 : 145
  • Jayaram , B. , Sharp , K. A. and Honig , B. 1989 . The electrostatic potential of B-DNA . Biopolymers , 28 : 975
  • Gordon , H. L. and Goldman , S. 1989 . Simulations on the primitive electrolyte environment of a high charge-density polyelectrolyte. A sampling problem and its solution . Molecular Simulation , 3 : 213
  • Torrie , G. M. and Valleau , J. P. 1980 . Electrical double layers. 1. Monte Carlo study of a uniformly charged suface . J. Chem. Phys. , 73 : 5807
  • Rhee , Y. J. , Halley , J. W. , Hautman , J. and Rahman , A. 1989 . Ewald methods in Molecular Dynamics for system of finite extent in one of three dimensions . Phys. Rev. B , 40 : 36
  • Manning , G. S. 1969 . Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties . J. Chem. Phys. , 51 : 924
  • Pohl , F. M. and Jovin , T. M. 1972 . Sat-induced Co-operative Conformational Change of a Synthetic DNA: Equilibrium and Kinetic Studies with Poly (dG-dC) . J. Mol. Biol. , 67 : 375
  • Valleau , J. P. 1989 . Flexible polyelectrolyte in ionic solution: a Monte Carlo study . Chem. Phys. , 129 : 163
  • Abascal , J. L. F. and Turq , P. 1991 . Cluster structure in model electrolyte solutions . Chem. Phys. , 153 : 79
  • Paulsen , M. D. , Richey , B. , Anderson , C. F. and Record , M. T. Jr. 1987 . The salt dependence of the preferential interaction coefficient in DNA solutions as determined by grand canonical Monte Carlo simulations . Chem. Phys. Lett. , 139 : 448

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