[gmx-users] protein-water distance restraints

[Francesco Oteri]

Dear Markus,
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.

Francesco


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
> Markus
>
>
>
>
>
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