Abstract
This application note presents gmx_ffconv, a command-line tool developed to facilitate the conversion of systems between all-atom force fields within GROMACS. As different force fields use their own naming conventions and atom ordering, force field conversion within GROMACS is usually a time-consuming, error-prone process. gmx_ffconv resolves atom ordering and naming mismatches between different force fields by reordering the coordinate file via molecular graph matching. This enables the use of identical starting coordinates across force fields, facilitating comparative simulations without requiring manual reordering or scripting. The tool has been validated on a broad range of systems, from small, nonstandard ligands to large, solvated heterogeneous systems with more than two million atoms. gmx_ffconv is available on GitHub: github.com/Jassu1998/gmx_ffconv.