[gmx-users] using position restraints

[Oliver Beckstein]

Hi Ken,

> 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.

Sorry to ask a trivial question but have you also got lines in your
topology like

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

The -DPOSRE in the mdp file only instructs the preprocessor to set the
flag POSRE, which in turn switches on the if branch in the top file. (The
topology is processed by cpp so anything that goes for cpp goes for top.)

The final test is analysing your tpr file, using gmxdump. 
  gmxdump -s md.tpr > md.txt
 
and search in md.txt for 

 functype[N]=POSRES

where N is the internal number of your restrained atom (might require some
detective work top find it). It tends to be in the last quarter of the
rather huge output. If it's not there then you don't have position
restraints.

hth
oli 

-- 
Oliver Beckstein * oliver at biop.ox.ac.uk
 http://sansom.biop.ox.ac.uk/oliver/