[gmx-users] trjconv -pbc atom -center rect

[Chih-Ying Lin]

Hi
I have a protein+several ligand in the simulation box.
After 5ns, the protein drift to the right edge of the box and the
ligand drift to the left edge of the box.

with this command =>
trjconv -pbc atom -center rect
the most part of the protein is still in the right edge of the box
the small part of the protein is shifted in the left edge of the box
and i can clearly see that the ligand attach onto the protein.


but, the protein is NOT in the center of the box ???

so, how can i use trjconv command to center protein and to see the
ligand attaching on the protein?


Thank you
Lin