[gmx-users] POPC simulation

[chris.neale at utoronto.ca]

> 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.