[gmx-users] Position restraints problem

Jernej Zidar jernej.zidar at gmail.com
Wed Mar 28 10:39:12 CEST 2012

On Wed, Mar 28, 2012 at 16:17,  <gmx-users-request at gromacs.org> wrote:
> See the warning in genrestr -h.
> If all you're doing is adding a single atom of position restraint per
> moleculetype, you can do that by hand faster than using make_ndx and
> genrestr and adding the #include.
> Mark

This in turn means genrestr is useless if one has more than one
molecule type. While I could set the restraints manually,
doing it by hand is not really an option if one has more than 100
entries. Ah well, bash magic to the rescue.

Jernej Zidar

For posterity reasons here's the warning:
WARNING: position restraints only work for the one molecule at a time.
Position restraints are interactions within molecules, therefore they should
be included within the correct [ moleculetype ] block in the topology. Since
the atom numbers in every moleculetype in the topology start at 1 and the
numbers in the input file for genrestr number consecutively from 1, genrestr
will only produce a useful file for the first molecule.

More information about the gromacs.org_gmx-users mailing list