[gmx-users] How to set the friction coefficient in BD?

eric jakobsson 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:
>Dear All,
>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
ph 217-244-2896
fax 217-244-2909
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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