# Gromacs MetaDump: a tool for extracting GROMACS simulation metadata

## TL;DR

GROMACS MetaDump is a tool that automatically extracts and standardizes metadata from GROMACS molecular dynamics simulations for easier data sharing and reuse.

## Contribution

Introduces GROMACS MetaDump, a novel tool for automated, standardized metadata extraction from GROMACS simulations.

## Key findings

- GROMACS MetaDump extracts simulation parameters like software version, force field, and temperature into structured JSON/YAML.
- The tool supports FAIR principles by making simulation datasets indexable and findable.
- Available as a web app, API, and command-line utility for broad accessibility.

## Abstract

The volume of molecular dynamics (MD) simulation data shared via public repositories is rapidly increasing; however, fragmentation across multiple independent repositories, each employing distinct dataset identifiers and metadata schemas, hinders the efficient exploration and reuse of these data. In this study, we present GROMACS MetaDump, a tool for automatic annotation of output files from GROMACS MD simulations producing human- and machine-readable metadata leveraging the native GROMACS metadata (gmx dump) output. The tool takes the run input simulation file (.tpr) as the basis for the metadata output, optionally extending it with annotations from topology and structure files (.top, .gro). The tool is available as a web application (https://gmd.ceitec.cz/), API service, and a command-line utility. By automating the metadata extraction process, GROMACS MetaDump aims to simplify and standardise the extraction of rich, structured metadata from GROMACS MD simulations, making it easier to share, discover, and reuse simulation data within the research community.

This work introduces GROMACS MetaDump, a software tool for the automatic extraction of metadata from molecular dynamics (MD) simulations performed with GROMACS. GROMACS MetaDump captures all extractable simulation parameters, such as software version, force field, water model, box geometry, temperature, etc., and returns them in a structured JSON or YAML file. As a result, GROMACS MetaDump supports the creation of unified metadata annotations of MD simulations, making datasets indexable and findable in line with the FAIR principles.