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
SMS schreiben mit WEB.DE FreeMail - einfach, schnell und
kostenguenstig. Jetzt gleich testen! *http://f.web.de/?mc=021192*
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
