[gmx-users] using position restraints

Sichun Yang syang at physics.ucsd.edu
Tue Oct 19 22:12:59 CEST 2004

hi Ken,

Just share my experiment,
since you have define = -DPOSRE,
make sure you used the corrent setup in your topology file
(note ifdef POSRE, no the default POSRES)

#ifdef POSRE
#include "./posre.itp"

Hope it helps.

On Tue, 19 Oct 2004, Ken wrote:

> 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...
> Thanks,
> Ken
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