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

User discussions
1

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.

2

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.

3

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:

image