[gmx-users] water in channel

Bert de Groot bgroot at gwdg.de
Tue Jan 20 10:10:01 CET 2004

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.


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

More information about the gromacs.org_gmx-users mailing list