distance restraint w/upper bound example

From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Mon Mar 05 2007 - 15:27:05 CST

I've been using NAMD for several years now, but never with
restraints. I'd like to impose a restraint on an atom-atom distance,
but cut off the restraint at an upper bound, something like:

if dist(atom1, atom2) < 12.0
        f=k/2(d - dr)^2
else
        f=0

I read the example script in the archive for a harmonic distance
restraint ( http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/
4984.html ), but I have no idea how to apply it to a bounded type
function. Could someone help me set up a script? (I've never even
used Tcl before) Thanks

Neema Salimi
nsalimi_at_msg.ucsf.edu

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143

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