However, if the candidate for the final graph contains disconnected subgraphs, a fifth step, shown in Figure , is necessary to analyze the relationships between them. This step begins by replacing all fragments-represented by disconnected subgraphs, except the largest-with coarse-grained (CG) particles positioned at each fragment's center of mass. The initial four steps are then repeated on this semi-CG system dataset to create a new graph with CG vertices corresponding to CG particles. The radius for edge creation around each CG particle is defined as the distance from its center of mass to its most distant atom plus the van der Waals radius of that atom. Once these steps are complete, each CG vertex is replaced by its original disconnected subgraph, with new connections added to each subgraph's vertices based on the CG vertex links. By the end of the fifth step, any previously missed interatomic connections are re-established, and the distinct fragments are identified. Whether the final graph was obtained after the fourth or the fifth step, it can be modified manually before searching for symmetries. Manual modifications can offer advantages in systems like the chemisorbed Pd/MgO-surface, see Figure . In this scenario, when a palladium atom becomes trapped in one of the numerous local minima, it can introduce bias into the final graph. Accordingly, the biased final graph does not have information associated with other local minimum configurations missing in the dataset. However, manual modifications applied to the final graph can help to restore the absent information in the trajectory to train a robust MLFF model. Therefore, being an optional step, the manual modifications can both compensate for insufficient configurational space sampling and include physical and chemical intuitions.