Hello Maria,
You can do it by two different methods.
1) You can increase the default VdW radii of the lipid atoms in
/usr/local/gromacs/share/top/vdwradii.dat file (path might be different from
your system), say 0.5 for carbon, so genbox will not add the water inside the
bilayer. but you will find a gap between lipid head groups and water molecules
which can be resolved after some ps dynamics. (I personally have not yet got
the success ;-) )
2) You can write a small script which can delete these water molecules, I wrote
a script for the same if you need contact me offline.
Hope it will help
Alok
----- Original Message -----
From: maria goranovic
To: gmx-users@gromacs.org
Sent: Sunday, October 21, 2007 3:57 PM
Subject: [gmx-users] solvate using genbox results in water in the center
ofthe bilayer. How to edit pdb file contents in gromacs ?
Hi
I am using editconf to try to add water layers on either side of my bilayer.
I use the following command:
genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs
spc216.gro -p topology.top
However, because the center of the bilayer region is less dense, a lot of
water molecules are created inside the bilayer.
- How does one usually edit pdb files in gromacs, in terms of, for example,
removing water molecules from the center of a bilayer ?
Thank you
-Maria
--
Maria G.
Technical University of Denmark
Copenhagen
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