[gmx-users] using position restraints
ksr at chemistry.umass.edu
Tue Oct 19 22:19:51 CEST 2004
Thanks for the quick response. Not at all trivial to me. My .top file
does indeed have the following lines:
I'm running on a Mac, so I'm not sure if the missing "./" prior to
"posre.itp" is significant.
However, I do not have a line in the gmxdump of my .tpr file of the form
Changed the line in my .top file to
and re-ran grompp. Still no line of type
So I clearly don't have any positional restraints. Any other ideas?
On Oct 19, 2004, at 3:46 PM, Oliver Beckstein wrote:
> 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
>> 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"
> 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.
> topology is processed by cpp so anything that goes for cpp goes for
> The final test is analysing your tpr file, using gmxdump.
> gmxdump -s md.tpr > md.txt
> and search in md.txt for
> where N is the internal number of your restrained atom (might require
> 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
> Oliver Beckstein * oliver at biop.ox.ac.uk
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