[gmx-users] protein-water distance restraints

[Justin A. Lemkul]

Markus Weingarth wrote:
> 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.
> 

Use the pull code.

-Justin

> Cheers
> Markus
> 
> 
> 
> 
>     ------------------------------------------------------------------------
>     *Von:* "Francesco Oteri" <francesco.oteri at gmail.com>
>     *Gesendet:* Oct 12, 2011 6:41:05 PM
>     *An:* gmx-users at gromacs.org
>     *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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> 
>          
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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