A GENERAL BROWNIAN DYNAMICS SIMULATION PROGRAM FOR BIOPOLYMER DYNAMICS AND ITS IMPLEMENTATION ON A VECTOR COMPUTER

A Brownian dynamics simulation program for the computation of transport properties of charged polarizable macromolecules is presented. The program contains routines for simulating polymer dynamics in a gel network as well as in a quiescent fluid or in a shear field. An electric field can also be included to simulate e.g., gel electrophoresis or electric dichroism. Vector algorithms have been used where possible to obtain maximum efficiency on a vector processor. The length of the vector registers and the effect of computer memory organization have also been considered. On an IBM 3090-150S VF, more than 1.5 . 10(6) steps are executed in one cpu hour for a chain with 128 subunits diffusing in a rigid gel consisting of 8828 beads.