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.
Cleaner method is to:
cp /usr/local/gromacs/share/top/vdwradii.dat ./vdwradii.dat
and then modify the local file.
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 ;-) )
Do I understand you to say that for you the gap does not completely
dissapear in <500ps? Did you use semiisotropic coupling? Otherwise it
will be more difficult for this space to fill in. It should fill in
really quite quickly (<<500ps)... has for me.
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.
I have previously posted such a script. It takes 10-30 minutes to run
since it's not sophisticated, but it does work very well.
http://www.gromacs.org/pipermail/gmx-users/2006-May/021526.html
I forgot to mention that in the previously referenced script there is
an assumption that you use a 3 atom water molecule. If you use tip4p
then you would want
if [ "$count" = 3 ]; then
count=0
fi
to be changed to:
if [ "$count" = 4 ]; then
count=0
fi
and etc for tip5p.
Hope it will help
Alok
----- Original Message -----
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
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