def METHOD_NAME(self, combined_system, molecule_name):
    combined_system.remove_molecule_type(molecule_name)
    # Just a sanity check
    combined_system.to_files(prefix=molecule_name, decimal=8)
    get_intermol_defaults(periodic=True).write_mdp_file("tmp.mdp")
    _process(
        _run_gmx_energy(f"{molecule_name}.top", f"{molecule_name}.gro", "tmp.mdp"),
    )