Switch RMSD analysis in `gather_rms_data` to the symmetry corrected RMSD.

[hannahbaumann]

For the HypTop protocol, this will require handling element changes between the core atoms in the end states.

state_lig = select_state_atoms(u, end_state="A").select_atoms("resname UNK")
# ToDo: Fix elements in the B state
fix_elements
guess_ligand_bonds(state_lig, delete_existing=True)
lig_rmsd = SymmetryCorrectedLigandRMSD(state_lig).run(step=skip)