How to center a molecule from an MD-simulation in Gromacs

center.sh

#!/usr/bin/env bash

TRAJIN=traj.xtc
TRAJOUT=trajfin.xtc

# delete the trajectory so gromacs wont display silly backup messages
if [ -e $TRAJOUT ]
then
  rm -f $TRAJOUT
fi

# center molecule (you will be asked!)
trjconv -pbc mol -center -ur compact -s md.tpr -f $TRAJIN -o tmp.xtc

# make everything rotate and translate around that molecule (you will be asked!)
trjconv -fit rot+trans -s md.tpr -f tmp.xtc -o $TRAJOUT

rm -f tmp.xtc