[gmx-users] POPC simulation
Mark.Abraham at anu.edu.au
Fri Nov 2 00:23:11 CET 2007
chris.neale at utoronto.ca wrote:
>> I want to perform peptide + popc membrane simulation. I download
>> popc128a.pdb from
>> 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:
> I and others also answered this question one week ago. Here is some info
> from that:
> This probable deserves a wiki entry.
Someone who actually does this sort of simulation should check it over
and expand as appropriate. Chris? Tsjerk?
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