An empirical boundary potential for water droplet simulations

An empirical modified boundary potential has been derived to correct the structural perturbations arising from the presence of the vacuum boundary in the simulation of spherical TIP4P water systems. The potential is parameterized for a 12.0‐Å sphere of TIP4P water and gives improved number density and orientational sampling behavior. It is also transferable to both larger and smaller simulation systems with only a moderate degradation in performance. Free‐energy calculations have been conducted for the perturbation of a TIP4P water molecule to methane under aqueous conditions, and the modified boundary potential gives results consistent with those from simulations using periodic boundary conditions. However, simple half‐harmonic boundary potentials give unsatisfactory number density, orientational sampling, and free‐energy results. Moreover, use of the modified boundary potential results in a negligible increase in simulation time. It is envisaged that the modified boundary potential will find use in free‐energy perturbation calculations on proteins with a solvent sphere centered on the active site. © 1995 by John Wiley & Sons, Inc.

[1]  D. Lide Handbook of Chemistry and Physics , 1992 .

[2]  William L. Jorgensen,et al.  Free energy of TIP4P water and the free energies of hydration of CH4 and Cl- from statistical perturbation theory , 1989 .

[3]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[4]  W. F. Gunsteren,et al.  The role of computer simulation techniques in protein engineering , 1988 .

[5]  M. Karplus,et al.  Deformable stochastic boundaries in molecular dynamics , 1983 .

[6]  M. Karplus,et al.  Stochastic boundary conditions for molecular dynamics simulations of ST2 water , 1984 .

[7]  Arieh Warshel,et al.  A surface constrained all‐atom solvent model for effective simulations of polar solutions , 1989 .

[8]  Alan C. Belch,et al.  Molecular dynamics simulations of tips2 water restricted by a spherical hydrophobic boundary , 1985 .

[9]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[10]  C. Brooks Computer simulation of liquids , 1989 .

[11]  D. Heyes,et al.  Electrostatic potentials and fields in infinite point charge lattices , 1981 .

[12]  W F van Gunsteren,et al.  On the interpretation of biochemical data by molecular dynamics computer simulation. , 1992, European journal of biochemistry.

[13]  A. H. Juffer,et al.  DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS , 1993 .

[14]  W. L. Jorgensen Free energy calculations: a breakthrough for modeling organic chemistry in solution , 1989 .

[15]  J. Mccammon,et al.  Molecular dynamics with stochastic boundary conditions , 1982 .

[16]  William L. Jorgensen,et al.  Hydration and energetics for tert-butyl chloride ion pairs in aqueous solution , 1987 .

[17]  Ronald M. Levy,et al.  Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models , 1989 .

[18]  J. Perram,et al.  Computer simulation of the static dielectric constant of systems with permanent electric dipoles. , 1986, Annual review of physical chemistry.

[19]  M. Neumann The dielectric constant of water. Computer simulations with the MCY potential , 1985 .