Re: [gmx-users] protein-water distance restraints

Wed, 12 Oct 2011 10:17:01 -0700

Hi Francesco,

Thanks for your answer, but that's not an option for me. I really would like to force the penetreation of a water-molecule into this cavity over the couse of the trajectory.

Cheers
Markus




Von: "Francesco Oteri" <[email protected]>
Gesendet: Oct 12, 2011 6:41:05 PM
An: [email protected]
Betreff: Re: [gmx-users] protein-water distance restraints

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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