GROMACS MetaDump: A tool to describe molecular dynamics simulations with powerful metadata

Molecular dynamics (MD) simulations generate vast datasets that are increasingly shared through public repositories, however, fragmentation and inconsistent metadata hinder their reuse. As a result, a vast majority of MD simulations is “technically accessible, but neither indexed, curated, or easily searchable” [1]. To address this problem, we present GROMACS MetaDump (https://gmd.ceitec.cz/), a software tool that automatically extracts, structures, and annotates GROMACS simulation files, producing rich and consistent metadata, capturing key descriptors such as simulation parameters, system setup, macromolecule identifiers (PDB, UniProt, PubChem), and administrative details. Without needing any manual input, the tool uses the simulation input file (.tpr) as the foundation, and optionally topology (.top) and structure (.gro) files, the tool produces human- and machine-readable outputs in JSON or YAML, which can be optionally edited. The mechanism behind the tool was validated on 4,364 publicly available GROMACS simulations and demonstrate its utility with two case studies: detailed annotation of Helicobacter pylori TonB-CTD simulations and large-scale analysis of repository trends. By standardising and automating metadata extraction, GROMACS MetaDump improves indexability and searchability of MD data, in line with the incentives of initiatives such as MDDB. GROMACS MetaDump is freely accessible as a web application, through API, and command-line utility, facilitating integration into diverse research workflows. [1]J. Tiemann, M. Szczuka, L. Bouarroudj, M. Oussaren, S. Garcia, R. Howard, L. Delemotte, E. Lindahl, M. Baaden, K. Lindorff-Larsen, M. Chavent, P. Poulain, eLife, 12, RP90061 (2024)