Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

bio.tools: an expanded web service for research software in the life sciences.

Nucleic acids research·2026
Same author

Foldify: Web Application for Protein Structure Prediction.

Journal of chemical information and modeling·2026
Same author

C-terminal long-QT type 1 R562S-Kv7.1 variant, the first variant in helix C impairing β-adrenergic response of the slow delayed rectifier K+ channel.

Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology·2026
Same author

MolMeDB RDF: transforming a relational database about biological membranes to the RDF format to increase interoperability.

Journal of cheminformatics·2026
Same author

PROPTIMUS LIVE: local constrained α-carbon optimization of proteins.

Nucleic acids research·2026
Same author

Dense yet flexible: how ladderanes found in anammox bacteria impact phospholipid membrane structure and properties.

Physical chemistry chemical physics : PCCP·2026
Same journal

ScrambleBench: a workflow for comparative assessment of structure-based de novo generative models.

Journal of cheminformatics·2026
Same journal

Smiles-based bioactivity prediction through molecular encoder selection and data augmentation.

Journal of cheminformatics·2026
Same journal

MINERVA: a public XAI-powered platform advancing multi-target discovery in Alzheimer's disease.

Journal of cheminformatics·2026
Same journal

Multimodal feature fusion for molecular property classification.

Journal of cheminformatics·2026
Same journal

P2MAT: A machine learning (ML) driven software for Property Prediction of MATerial.

Journal of cheminformatics·2026
Same journal

Computational design of low-volatility lubricants for space using interpretable machine learning.

Journal of cheminformatics·2026
See all related articles

Related Experiment Video

Updated: Jan 6, 2026

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.0K

Gromacs MetaDump: a tool for extracting GROMACS simulation metadata.

Adrián Rošinec1,2,3, Terézia Slanináková4,5, Tomáš Pavlík2,3

  • 1CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.

Journal of Cheminformatics
|October 24, 2025
PubMed
Summary
This summary is machine-generated.

GROMACS MetaDump automatically extracts metadata from molecular dynamics (MD) simulations. This tool enhances the findability and reusability of GROMACS simulation data, adhering to FAIR principles.

Keywords:
FAIRGROMACSGROMACS MetaDumpMetadata extractionMolecular dynamicsSimulation annotations

More Related Videos

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.1K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.5K

Related Experiment Videos

Last Updated: Jan 6, 2026

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

3.0K
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.1K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.5K

Area of Science:

  • Computational chemistry and biophysics
  • Bioinformatics and cheminformatics
  • Scientific software development

Background:

  • Molecular dynamics (MD) simulation data is rapidly growing but fragmented across repositories.
  • Lack of standardized metadata hinders data exploration and reuse.
  • Existing methods for metadata extraction are often manual and inconsistent.

Purpose of the Study:

  • To introduce GROMACS MetaDump, a tool for automatic metadata extraction from GROMACS MD simulations.
  • To standardize and simplify the creation of human- and machine-readable metadata.
  • To improve the findability and reusability of MD simulation data in line with FAIR principles.

Main Methods:

  • Developed GROMACS MetaDump to process GROMACS output files (.tpr, .top, .gro).
  • Leverages native GROMACS metadata (gmx dump) for extraction.
  • Provides metadata in structured JSON or YAML formats.
  • Offers web application, API service, and command-line utility.

Main Results:

  • GROMACS MetaDump captures comprehensive simulation parameters (software version, force field, box geometry, etc.).
  • Automated extraction ensures consistent and rich metadata.
  • Facilitates unified metadata annotations for GROMACS simulations.

Conclusions:

  • GROMACS MetaDump simplifies and standardizes metadata extraction for GROMACS MD simulations.
  • The tool enhances data sharing, discovery, and reuse within the research community.
  • Supports the FAIR data principles by making simulation datasets indexable and findable.