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" <[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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--
========================================
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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