Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F25%3A73633244" target="_blank" >RIV/61989592:15310/25:73633244 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14310/25:00142353
Result on the web
<a href="https://link.springer.com/article/10.1186/s13321-025-01082-5" target="_blank" >https://link.springer.com/article/10.1186/s13321-025-01082-5</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s13321-025-01082-5" target="_blank" >10.1186/s13321-025-01082-5</a>
Alternative languages
Result language
angličtina
Original language name
Gromacs MetaDump: a tool for extracting GROMACS simulation metadata
Original language description
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 contributionThis 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.
Czech name
—
Czech description
—
Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Cheminformatics
ISSN
1758-2946
e-ISSN
—
Volume of the periodical
17
Issue of the periodical within the volume
1
Country of publishing house
GB - UNITED KINGDOM
Number of pages
10
Pages from-to
"160-1"-"160-10"
UT code for WoS article
001598802000001
EID of the result in the Scopus database
2-s2.0-105019521041