In Gromologist, topologies can be matched with a compatible structure, so that where relevant, topology operations can be simultaneously performed on the structure attribute (and vice versa), facilitating the work with simulation-ready systems, and fully leveraging the information available in both files. Examples of such procedures include atom addition/removal, or introduction of mutations. When a topology is available, chain assignment can be made using molecule definitions therein. Moreover, when Gromacs often only indicates an unspecified mismatch between e.g. the number of atoms in structure and topology, Gromologist provides a specific list of all unmatched atom names, facilitating the identification of missing atoms or residues in either one.