Run make_tpr.sh followed by run_md.sh. This will create three trajectories:

1. cpeptide_md.trr - the no-forces trr. No forces are written to this trajectory.
2. cpeptide_md-with-forces.trr - the with-forces trr. Forces are written to this trajectory.
3. cpeptide_md-rerun.trr - created by mdrun -rerun, using the with-forces tpr on the no-forces trr

If all goes well, the forces in cpeptide_md-with-forces.trr and cpeptide_md-rerun.trr should be identical.

• A quick script to compare the forces in cpeptide_md-with-forces.trr and cpeptide_md-rerun.trr, using gmxdump/g_traj and diff.