To compare how similar two molecular structures are, an easy method is to simply compute the Root Mean Square Deviation (RMSD) between the two geometries. This can be done by finding the optimal rotation matrix between the two structures using fx. the Kabsch algorithm 85 before computing the actual RMSD. This works well for small systems, but for large systems, such as molecular clusters, this can quickly "hide" small differences. An example of this could be an ammonia molecule inside a multi-component cluster: If all other monomers are largely the same, but the ammonia sits in a different orientation it is technically a different configuration, but as there are only 4 atoms in ammonia this deviation contributes very little to the overall RMSD.