[gmx-users] How to set the friction coefficient in BD?
jake at ncsa.uiuc.edu
Mon Sep 6 22:26:18 CEST 2004
In computing the size of a random thermal jump, the friction coefficient
and the size of the time step both appear in the expression so that they
can't be separated.
At 06:38 AM 9/6/2004, you wrote:
>When I do the BD simulation I want to know how to set the value of friction
>coefficient. Should I need to determine it according to the viscosity of
>the solvents such as water and alcohol. Or should I try some value first in
>BD, then get some property of the system and compare it with experiment
>I read some pages in Hess's book. He said like this:"In Brownian dynamics
>the friction coefficient scales the time. This means that one
>only needs to perform a simulation at one value of friction coefficient .
>Afterwards the time of the results can be scaled to obtain results for any
>value of friction coefficient ."
>I did not catch the meaning of it. Does it mean that only one friction
>coefficient is ok? However, different solvents have different property,
>right? How can I get the differences if I just set one friction coefficient
>in BD simulation?
>Thx a lot.
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Eric Jakobsson, Ph.D.
Professor, Molecular and Integrative Physiology, Biophysics and
Computational Biology, Beckman Institute, Bioengineering, Biochemistry, and
Senior Research Scientist, National Center for Supercomputing Applications
4021 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Avenue
Urbana, IL 61801
e-mail jake at ncsa.uiuc.edu
(Since May 2003 I have been on leave from the University of Illinois to
serve as the Chair of the NIH Biomedical Information Science and Technology
Consortium and the NIGMS Center for Bioinformatics and Computational
Biology, in Bethesda, Maryland. However I commute to Urbana almost every
week to maintain my research lab here.
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