The RMSDs here are computed using 'calculate_rmsd' (https://github.com/charnley/rmsd) on which clusttraj is build upon.
We perform many steps to mimick how clusttraj behaves, computing the RMSDs at each step.
The RMSDs are always computed between 'conf1.xyz' and another configuration.
In parenthesis, we have the CLI options passed to calculate_rmsd.


1)
conf2: 5.885716603626963 ('-r none')

Generate configuratin with superposition of solute with '-r kabsch --add-idx 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 -p'.
Then compute the RMSDs between conf1.xyz and this configuration with:

2)
conf2_superp1: 3.601404699478113 ('-r none')
3)
conf2_superp2: 0.36862451 ('-r none -e --reorder-method hungarian')
4)
conf2_superp3: 0.26873082 ('-r kabsch -e --reorder-method hungarian')


The 'direct approach' gives:
5)
calculate_rmsd conf1.xyz conf2.xyz -r kabsch:  3.593388899340819
6)
calculate_rmsd conf1.xyz conf2.xyz -r kabsch -e --reorder-method hungarian:  3.0174458935459287
7)
calculate_rmsd conf1.xyz conf2.xyz -r kabsch -e --reorder-method inertia-hungarian:  2.646836715126581

