On 28/03/2012 7:39 PM, Jernej Zidar wrote:
On Wed, Mar 28, 2012 at 16:17,<[email protected]> 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 :-)
Mark
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.
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
