Answer to this quetion lies with the periodic boundary conditions which you have applied in the .mdp file.

" Multimeric systems are difficult for any PBC routine in any software to deal with.  The quickest solution is probably (1) make the molecules whole as you have done and then (2) center on interfacial residues belonging to one monomer, via a custom index group.  Doing this will put the interface of the dimer at (or at least, extremely close to) the center of the box, with both monomers in the unit cell.", Justin Lemkul

Or follow this question-

How to remove GROMACS periodic boundary conditions?

https://www.researchgate.net/post/How_to_remove_GROMACS_periodic_boundary_conditions

You should extensively use gmx trjconv tool for removing PBC of the system. I recommend you as following steps.

1. trjconv -pbc nojump

2. trjconv -pbc mol -ur compact -center (center specific amino acid or molecule)

If it is only for display purpose in VMD, you may use:

For a single frame

pbc wrap -center origin -compound fragment -shiftcenterrel "$x $y $z"

Hi Batsaikhan Mijiddorj , in my case I have 10 monomers inside a box and I have tried all these options. Do you know how else I can fix this pbc problem? because it is affecting my analysis.

Hi,

1. You should center one of the monomers.

2. nojump

3. -pbc mol

if necessary, you should use pbc atom and pbc res before -pbc mol.

Hi Batsaikhan Mijiddorj I used one of the monomers as the center already but when I load the pdb file, the protein is broken. With no jump, the protein was jumping out of the box.

These are the commands I have used so far :

gmx trjconv -f md.xtc -s md.tpr -o md_protein.xtc - index.ndx -center ( picked one of the monomers as center and output the protein.

trjconv -f md.xtc -s md.tpr -o md_protein.pdb -index.ndx - center -dump 0 ( did same as above)

trjconv -f md_protein.xtc -s md_proein.pdb -pbc no jump ( output protein)

can you test following steps?

1. -pbc nojump

2. -center (correct atom or monomer)

3. -pbc atom

4. -pbc res

5. -pbc mol

Perhaps, this sequence of commands could be overlong. I hope that it will work for you. Otherwise, I do not have any idea.