Placement of molecules in the corners of the simulation box. Why?

GROMACS version: 2019.4

Hi. I did 200 ns MD simulation for self assembly of a number of peptides.
Why are my peptides placed in the corners of the box during the simulation??
In the case of articles similar to my work, even in shorter times,
I saw that the molecules get closer to each other and are placed inside the box during the simulation and at the end of the simulation. I even fixed the pbc problem with the trjconv command twice and the following options:

  1. trjconv -pbc nojump

  2. trjconv -pbc mol -center

Did I make a mistake in solving the pbc problem? If anyone has a similar experience, I would be grateful if you could help me.

You need to make an index group corresponding to one chain and choose it for centering with trjconv. That will wrap the other peptides into the central image.

Dear jalemkul,

I did what you said:

  1. I Made an index group corresponding to one chain.
  2. I chose it for centering with trjconv using the following command:
    gmx_mpi trjconv -f md.xtc -s md.tpr -n ndx.ndx -o central.xtc -center

But problem was not solved: