PBC correction doesn't remove all PBCs

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GROMACS version: 2021.4
GROMACS modification: No

Hi,

I can’t correct the PBC of my system after the MD simulation. My system includes a monomer protein, POPC membrane bilayer, and ligand.
It was relatively stable and didn’t show any other problems in VMD.

Based on Terminology — GROMACS 2022.3 documentation.

My commands:

gmx trjconv -f step7.gro -s step7.tpr -o step7whole.xtc -n indexPL.ndx -pbc whole -b 110000 -e 210000
System(0)

I didn’t use the cluster command.

gmx trjconv -f step7whole.xtc -s step72.tpr -o step7noPBC.xtc -n indexPL.ndx -pbc nojump
System(0)

gmx trjconv -f step7noPBC.xtc -s step72.tpr -o final2.xtc -n indexPL.ndx -pbc mol -center
Protein and ligand as the center, write output into System (0)

I also read this topic Correcting Periodicity in GMX. But it didn’t help.

The commands reduced my PBC, but I still see them in the final file frames.

I appreciate any kinda help. Thanks!