[gmx-users] using position restraints

Ken ksr at chemistry.umass.edu
Tue Oct 19 21:09:09 CEST 2004

Hello all,

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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