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

Victor Rosas Garcia rosas.victor at gmail.com
Sat Jul 7 20:59:45 CEST 2018

try "-pbc whole" instead of "-pbc mol"

El sáb., 7 jul. 2018 a las 2:13, Anjana Jayasinghe (<anjusilva90 at yahoo.com>)

> 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.
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