[gmx-users] bilayer & genbox/editconf

Chris Shaw chrisbiochem at yahoo.co.uk
Thu Nov 21 13:25:23 CET 2002

Hi all, 

Just a quick one , I hope. I am trying to simulate a set of proteins in a bilayer. I have downloaded the bilayer from Peters web page. My problem is some of my proteins are "too big" for the lipid/solvent and poke out of the top & bottom. I have tried to use both editconf & genbox to extend the box in the z direction with the box command using the existing x & y coords and using a larger z value ( no -d flag). when I then use genbox i get a layer of water surrounding the entire simulation box or I get a few water atoms surrounding the parts of the protein which "poke" out. My question is how do I increase the z coords to give a uniform layer of water on the extisting simulation box. 



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