A general Brownian dynamics simulation program for biopolymer dynamics and its implementation on a vector computer

✍ Scribed by Christer Elvingson

• Publisher: John Wiley and Sons
• Year: 1991
• Tongue: English
• Weight: 654 KB
• Volume: 12
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540120108

✦ Synopsis

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 3090-1503 VF, more than 1.5 . lo6 steps are executed in one cpu hour for a chain with 128 subunits diffusing in a rigid gel consisting of 8828 beads.