[EMAIL PROTECTED] wrote:
Hi
I want to perform peptide + popc membrane simulation. I download
popc128a.pdb from
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
Before I introduce the peptide into the membrane, the water layer
had to be broadened to ensure full solvation of the peptide .I
increase the water layer using the following commands
1. editconf -f popc128a.pdb -o po_box.pdb -box 6.1065
6.1059 9.0000 -c
2. genbox -cp po_box.pdb -cs -o po_sol.pdb -p lip.top
Now, the no. of water molecules over the bilayer increased . But,
the problem is that there are water molecules inside the bilayer,
which were absent incase of popc128a.pdb. How can I remove these
offending water molecules?
Did you search?
Search "water membrane" = first hit:
http://www.gromacs.org/pipermail/gmx-users/2007-March/026289.html
I and others also answered this question one week ago. Here is some info
from that:
http://www.gromacs.org/pipermail/gmx-users/2007-October/030361.html
http://www.gromacs.org/pipermail/gmx-users/2007-October/030400.html
This probable deserves a wiki entry.
Done... http://wiki.gromacs.org/index.php/Membrane_Simulations
Someone who actually does this sort of simulation should check it over
and expand as appropriate. Chris? Tsjerk?
Mark
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