[gmx-users] protein-water distance restraints
francesco.oteri at gmail.com
Wed Oct 12 18:41:05 CEST 2011
If you know the residues composing the cavity (and I think you know it),
you can simply change the coordinates
of the water molecule in the .gro file to move the water in the cavity.
Il 12/10/2011 18:17, Markus Weingarth ha scritto:
> Dear Gromacs-users,
> I would like to force an arbitrary water molcule from the box into an
> occluded cavity of a membrane-channel. It do not want this water
> molcule within the cavity at the beginning of the simulation.
> I though that I could implement intermolecular distance restraints
> between a water residue an the protein, but I did not manage that and
> all the suggestions I found here to implement intermolecular distance
> restraints seem not to work out for water - protein contacts. Does
> anybody has a suggestion how to implement such restraints ? Would the
> pull-code an option for my problem ?
> Thank you very much
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