[gmx-users] water in channel

[Bert de Groot]

Anton Feenstra wrote:

>  From what I hear, water inside bilayers occur often when using genbox.
> Some people argue about whether it is a problem, but usually the only
> way to solve it is to remove them 'manually'. That is probably easier
> than it sounds, based on the Z coordinate you can easily identify them,
> but then you include some at the center of the protein. THese you can
> identify by now looking at the location in the x-y plane, or you could
> look at their distance to the protein. Probably, some of the membrane-
> guru's have scripts that may make this easier...
> 

I've always used genbox. Its behaviour can be adapted by modifying
vdwradii.dat. When you explicitly put the lipid tail atoms in the file with
a reasonably large radius, almost no waters will be iserted in the
lipid tail region. You might still want to remove a few waters manually
afterwards though.

Bert

ATTENTION: Please note new phone/fax numbers below!

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
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