Bonds and atoms. Primitive operations on topologies include adding, removing or swapping atoms in molecules while preserving a correct numbering scheme across all sections. Adding or removing bonds is also supported, including new bonds between two molecules, in which case the two become merged into a single molecule entry, and all new bonded terms (pairs, angles, dihedrals) are automatically identified and added, while existing ones are preserved and renumbered correctly. This allows for easy creation of chemical adducts or cyclic molecules, as well as editing of protonation states or simple chemical modifications without the need of extending the basic residue library (.rtp/.hdb files). Another heavily requested feature was the automated introduction of ,,special bonds" -disulfides and transition metal coordination bonds -that are not always correctly guessed by default Gromacs tools. Finally, Gromologist also provides a low-level interface for the mutation library, and can be easily incorporated into custom modification workflows.