From: Axel Kohlmeyer (
Date: Mon Jul 22 2019 - 11:58:08 CDT

-compound residue is not always sufficient to keep molecules intact.
please try -compound fragment instead.


On Mon, Jul 22, 2019 at 9:09 AM Maryam X <> wrote:

> Dear all,
> I have a system of 10 monomers in a simulation box trying to study
> aggregation and I ran my simulation using gromacs.
> However, after the simulation, I noticed that I have periodic boundary
> conditions i.e. some of my molecules were broken and I also noticed some
> unwanted bonds/lines showing when I play the trajectory movie in VMD. I
> have tried to solve the issue using trjconv (gromacs) but its not fixed.
> I also read through the Vmd mailing list and followed the instructions I
> found but the problem persists. Can someone please help?
> I will list the commands I have tried thus far below using vmd:
> Pbc unwrap (this removed the bonds and made the protein whole but the the
> protein went out of the box)
> Pbc wrap -compound -all (to move the proteins back inside the box), butv
> this did not completely solve the problem.
> I have also tried
> *pbc wrap -center com -centersel "protein and chain A" -compound residue
> -all*
> *pbc wrap -center com -centersel "protein " -compound residue -all*

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.