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A general Brownian dynamics simulation program for biopolymer dynamics and its implementation on a vector computer
Author(s) -
Elvingson Christer
Publication year - 1991
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540120108
Subject(s) - brownian dynamics , electric field , molecular dynamics , computation , dynamics (music) , computer science , brownian motion , biopolymer , computational science , parallel computing , statistical physics , algorithm , chemistry , physics , polymer , computational chemistry , nuclear magnetic resonance , quantum mechanics , acoustics
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.
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