[gmx-users] How to get the complete molecule?

[Anjana Jayasinghe]

Dear All,
In my simulation, part of my molecule is in a one cell and the other part is in the adjacent cell. I want to get the complete molecule in the pdb format in the center of the box. I tried to do that using gmx trjconv -f run.pdb -s run.tpr -pbc mol -ur compact -center -o run_new.pdbBut I couldn't get what I want. Can anyone help me?
Thank you.