From: Maryam X (
Date: Mon Jul 22 2019 - 07:38:47 CDT

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
*pbc wrap -center com -centersel "protein " -compound residue -all*