A slower but more accurate option is to compare root-mean-squared displacement (RMSD) between two identically oriented structures, which utilizes a modified version of the ArbAlign program. Finally, we provide the selection method introduced by Kubečka et al., which selects a subset of the most distinct configurations from a large data set. This representative subset of configurations might result in not finding exactly the global minimum at the desired final level of theory, however, the best of the selected structures will be close to the real global minimum structure. Such a method is especially useful for large clusters, for which many low-lying energy minima are thermodynamically populated due to small energy gaps between them.