[gmx-users] bilayer & genbox/editconf

Rainer Boeckmann rboeckm at gwdg.de
Thu Nov 21 15:20:40 CET 2002

Hi Chris,

..did you center the system prior to extending the box? You could also extend
the box editing the box size in the pdb-file and then using genbox. By the way,
genbox will also place some water molecules inside the bilayer.  You could
prevent this by chosing larger radii for the bilayer atoms in vdwradii.dat.


Chris Shaw wrote:

> Hi all,
> Just a quick one , I hope. I am trying to simulate a set of proteins in a
> bilayer. I have downloaded the bilayer from Peters web page. My problem is
> some of my proteins are "too big" for the lipid/solvent and poke out of the
> top & bottom. I have tried to use both editconf & genbox to extend the box in
> the z direction with the box command using the existing x & y coords and using
> a larger z value ( no -d flag). when I then use genbox i get a layer of water
> surrounding the entire simulation box or I get a few water atoms surrounding
> the parts of the protein which "poke" out. My question is how do I increase
> the z coords to give a uniform layer of water on the extisting simulation box.
> Cheers
> Chris
> -------------------------------------------------------------------------------
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Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

Tel.: +49(551)201-1141, Fax.: +49(551)201-1089
email: rboeckm at gwdg.de


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