I've been trying to find the definition of the cluster application's -gdtmm flag, and why we might use it over clustering by rmsd (no flag required).
All the examples I've run across use the -gdtmm flag, but again, I'm just not how exactly this is clustering.
Then, following that, when the flag -cluster:sort_groups_by_energy is used, how does it sort them? Does it label the first cluster as the one with the lowest average energy for all the structures in the cluster? It almost seems at odds with clustering by RMSD.