From: Olaf Lenz (
Date: Mon May 16 2011 - 03:14:25 CDT


On 05/13/2011 08:50 PM, cnu gromacs wrote:
> To avoid the possible artifacts caused by the lipid bilayer motion,
> using PBC wrap for each frame i aligned center of lipid bilayer to
> the center of unit cell, and recorded the protein coordinates with
> the following commands.
> pbc wrap -centersel "lipid" -center com -compound res -all animate
> write dcd protein.dcd beg 0 end -1 sel $protein
> Although the commands worked without any error. It does not seem to
> be giving me the transformed coordinates (corrected with lipid
> bilayer motion). The calculated COM of the protein before and after
> use of pbc wrap is same. Can any body hint me, What would have gone
> wrong?

I believe that you have misunderstood what "pbc wrap" does.

"pbc wrap" will only modify coordinates of an atom if the atom has to be
wrapped, i.e. if it is not within the specified unitcell. It will not
modify the coordinates of atoms that are already in the unitcell at all!
In your case, this means that a few of the lipids close to the boundary
of the system will be wrapped, however the protein (which is probably
close to the center of your system) will remain completely untouched.
Therefore you do not observe any changes in the proteins coordinates.

PBCTools cannot help you. Usually, what you want to do should be done by
the simulation tool in some way or the other.


Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Pfaffenwaldring 27, D-70569 Stuttgart
Phone: +49-711-685-63607