From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Feb 06 2004 - 14:34:50 CST
It's probably easiest to do this in TclForces, making each molecule an
atom "group" and applying constraining forces to the COM of each group.
Be careful, since TclForce uses 1-based atomids and VMD is 0-based.
On Wed, 4 Feb 2004, Hyonseok Hwang wrote:
> Dear all,
> We know that we can set up a distance constraint between the center of
> masses of two molecules for the calculation of the potential of mean
> force. What I want to do is to set up the distance constraint between
> the COM of two molecules in my MD simulation, but I don't want to
> calculate the PMF. In this case, should I use the same configuration
> file as I do for the PMF calculation and then just ignore the PMF
> calculation part in the output file?
> Thanks a lot!
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