ArticleJournal of cheminformatics2025
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata.
Article in Journal of cheminformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Single-Residue Substitution of Opicalcin1 Enhances Cellular Uptake but Reduces CaChembiochem : a European journal of chemical biology · 2026Article
- Immunoinformatics-driven design of a multi-epitope vaccine againstFrontiers in immunology · 2026Article
- Integrated bioinformatics and experimental validation identifies SOX2 as a key therapeutic target for chronic atrophic gastritis/gastric cancer-depression comorbidity.Frontiers in oncology · 2026Article
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Authors and funding
12 authors.
Funding
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. SCIENTIFIC CONTRIBUTION: 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.