[gmx-users] using position restraints
ksr at chemistry.umass.edu
Tue Oct 19 21:09:09 CEST 2004
I need some help with what is certainly a trivial problem. I want to
apply a positional restraint to a single atom in a molecule that I am
simulating. The restraint file, posre.itp is generated from pdb2gmx.
Upon viewing this file I found that the force constants at all
positions were set to x,y,z = 1000,1000,1000. I changed this such that
a single atom had a restraint force constant of 1000,1000, 1000 and the
rest were 0,0,0. I modified my .mdp file to include define = -DPOSRE
and ran a short test simulation.
Upon viewing the trajectory I found that the molecule drifted freely
about the box, showing no restraint, if you will. As a further test I
generated another posre.itp file and left the restraints all at 1000,
1000, 1000. The test simulation again showed motion, both translational
and within the chain. I've searched the site as well as my own archive
of gmx-users e-mails, to no avail. If someone could show me the error
in my ways...
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