[gmx-users] POPC simulation

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Nov 1 17:46:33 CET 2007

> 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:

I and others also answered this question one week ago. Here is some  
info from that:

This probable deserves a wiki entry.

More information about the gromacs.org_gmx-users mailing list