RE: force calculation during to conformational change

From: Pijush Ghosh (
Date: Tue Jul 11 2006 - 17:37:51 CDT

Hi Gaurav
   This is just an idea, may be somebody can comment on it or correct me.
For example you want to find the force of separation between two groups of
atoms (one on each strand). Find the plot of their interaction energy with
their displacement. The slope of this energy displacement curve can give you
a good estimate of the force experienced by those groups, if not the exact
   I would look forward for some discussion on this.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA

-----Original Message-----
From: [] On Behalf
Of Gaurav Sharma
Sent: Tuesday, July 11, 2006 11:38 AM
Subject: namd-l: force calculation during to conformational change

Hi All,

I have a peptide system consisting of two parallel alpha-helical chains.
The chains move away from each other during MD run due to repulsive
forces from ionized histidines on both chains. I would like to calculate
the force by which the chains move apart. Any idea how I can do this
using NAMD?

Thanks for your help.

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