ELECTROSTATICS AND DIFFUSION OF MOLECULES IN SOLUTION - SIMULATIONS WITH THE UNIVERSITY-OF-HOUSTON-BROWNIAN DYNAMICS PROGRAM

Brownian dynamics simulations are not new, but typically programs have been written for specific systems. In this paper, we describe a general-purpose Brownian dynamics program that has been developed at the University of Houston. The program can simulate the diffusion of flexible chains. The rates of diffusion-controlled reactions can be calculated for arbitrary reaction geometries. Electrostatic interactions among the diffusing species are modeled by the use of finite difference solutions of the linearized Poisson-Boltzmann equation. The program can also be used for electrostatic force and energy calculations. Provisions are made for coordinate and parameter manipulations. The basic structure of the program and its functionality are discussed and some example applications are cited.