[gmx-users] center an atomic group

Dr. Vitaly V. G. Chaban vvchaban at gmail.com
Thu Jun 21 21:20:44 CEST 2012

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.

Thank you.

Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216

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