[gmx-users] center an atomic group

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 21 22:17:48 CEST 2012

On 6/21/12 3:20 PM, Dr. Vitaly V. G. Chaban wrote:
> Dear All -
> I have a macromolecule surrounded by multiple layers of water in my
> box. For visualization purposes, I would like to center the
> macromolecule in the box (PDB file), so that its geometrical center
> coincides with the geometrical center of the cubic box (as
> visualization utilities undertand this center).
> Would anyone please suggest a handy route within the gromacs utilities
> to achieve this? I tried to use
> editconf -center $macromol_center_coords -f conf.gro -o conf.pdb
> I am not sure what it exactle does, but the macromolecule was not at
> the center of the box.

In the absence of setting a box, the editconf approach may not work.  I use 
-center and -box in concert to position solutes in a box, though I don't know, 
in principle, why this doesn't work.

trjconv -center is designed to do exactly what you're looking for.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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