DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the surface on the dynamics of the atoms inside the surface. The boundary atoms can move but are position restrained. A simple application to liquid argon in a sphere is demonstrated. The methodologies are illustrated for calculating the radial distribution function, density, pressure, potential energy per atom and chemical potential. Also the velocity autocorrelation function and the diffusion constant are calculated. To derive the parameters of the model an empirical approach was followed which consisted of comparing the simulation results of the boundary model with simulation results using periodic boundary conditions. The conclusion is that the present method is able to reproduce the dynamical, structural and thermo...

[1]  R W Hockney,et al.  Computer Simulation Using Particles , 1966 .

[2]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[3]  J. W. Perram,et al.  Simulation of electrostatic systems in periodic boundary conditions. III. Further theory and applications , 1983, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[4]  R. Zauhar,et al.  The rigorous computation of the molecular electric potential , 1988 .

[5]  Kim A. Sharp,et al.  Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method , 1991 .

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

[7]  L. Verlet,et al.  Computer "Experiments" on Classical Fluids. III. Time-Dependent Self-Correlation Functions , 1970 .

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

[9]  B. Widom,et al.  Some Topics in the Theory of Fluids , 1963 .

[10]  K. Shing,et al.  The chemical potential in dense fluids and fluid mixtures via computer simulation , 1982 .

[11]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

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

[13]  J. Kirkwood,et al.  The Statistical Mechanical Theory of Transport Processes. IV. The Equations of Hydrodynamics , 1950 .

[14]  J. Henderson,et al.  Statistical mechanics of inhomogeneous fluids , 1982, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[15]  J. G. Powles,et al.  Non-destructive molecular-dynamics simulation of the chemical potential of a fluid , 1982 .

[16]  C. F. Curtiss,et al.  Molecular Theory Of Gases And Liquids , 1954 .

[17]  Aneesur Rahman,et al.  Correlations in the Motion of Atoms in Liquid Argon , 1964 .

[18]  Michael L. Connolly,et al.  Molecular surface Triangulation , 1985 .

[19]  A. J. Stam,et al.  Estimation of statistical errors in molecular simulation calculations , 1986 .

[20]  D. J. Tildesley,et al.  Equation of state for the Lennard-Jones fluid , 1979 .

[21]  W F van Gunsteren,et al.  Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: Application to the DNA binding domain of lac repressor from Escherichia coli , 1988, Proteins.