[gmx-users] Position restraints problem

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 28 13:49:08 CEST 2012

On 28/03/2012 7:39 PM, Jernej Zidar wrote:
> 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.

It's pretty rare to have more than a handful of [moleculetype] sections, 
each of which would want customized [position_restraints]. pdb2gmx will 
write all-heavy-atom [position_restraints] sections which serve most 
purposes. It would not be hard to modify genrestr to be useful in the 
general case, but until a developer needs it badly enough, it'll be a 
low priority :-)


> Thanks,
> 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.

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