Gromacs is a popular open-source software tool biologists and chemists use to simulate molecular dynamics. It is widely used for simulating complex biological processes, including protein folding and drug interactions. However, despite its popularity and usefulness, Gromacs lacks proper support for the FAIR (Findable, Accessible, Interoperable, and Reusable) principles when publishing output datasets. Specifically, it lacks support for generating a proper metadata description for each dataset, making it difficult for researchers to find and reuse the data stored in online archives.

This bachelor's thesis aims to analyze the Gromacs dump tool gmx dump and try to add support for outputting metadata in JSON or YAML data file format.

The goals of this thesis are:

• A comprehensive analysis of the current state of metadata support in Gromacs and the gaps that need to be addressed.
• An updated gmx dump tool that supports metadata generation in JSON or YAML data file format.
• Contribute changes to the Gromcas tool community.
• A testing report of the updated gmx dump tool and its effectiveness in generating metadata for Gromacs output datasets.
• A set of recommendations for future work to improve the FAIRness of Gromacs output datasets.