[gmx-users] centering

[Marc Vogt]

I've read the archives and I've been trying to center a solute
in a box with solvent and I still can't do it.  I have a pdb file
from a trajectory that looks something like this:

	wwwww
	wwwww
	 wwppp
	wwwww
	wwwww

w is water and p is protein

I want:

	wwwww
	wwwww
	wpppw
	wwwww
	wwwww


The box is 50 Angstroms x 50 Angstroms x 50 Angstroms.
I tried
editconf -f start.pdb -o centered.pdb -center 2.5 2.5 2.5
and 
editconf -f start.pdb -o centered.pdb -c

and different versions of gromacs but the resulting centered.pdb always 
looks like the starting one.  Seems like it should be easy and I'm sure
it's something stupid, but I can't get it.

thanks,
Marc