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

Molecular Models02:00

Molecular Models

42.7K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
42.7K

You might also read

Related Articles

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

Sort by
Same author

Crops exposed to extreme conditions: perspectives of gene editing to improve stress tolerance.

Plant cell reports·2026
Same author

Luminescent heparin-functionalized carbon dots with potential applications in nanoparticle-protein interactions and cell imaging.

Scientific reports·2026
Same author

Marine-Derived Dual BTK-FGFR Inhibitors: Pioneering a New Era of Precision Oncology Therapeutics.

Anti-cancer agents in medicinal chemistry·2026
Same author

Deciphering the multi-organ anti-fibrotic mechanisms of pirfenidone and nintedanib via network pharmacology.

Personalized medicine·2026
Same author

Novel class of population mean estimators based on robust regression methods.

Scientific reports·2026
Same author

Unraveling the Multifunctional and Translational Paradigm of Nanoparticulate Systems against Colorectal Cancer.

ACS applied bio materials·2026

Related Experiment Video

Updated: Nov 20, 2025

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

773

HeroMDAnalysis: an automagical tool for GROMACS-based molecular dynamics simulation analysis.

Ravi Rawat1, Kamal Kant1,2, Anoop Kumar1

  • 1Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215, India.

Future Medicinal Chemistry
|January 26, 2021
PubMed
Summary

HeroMDAnalysis simplifies molecular dynamics simulations (MDS) analysis for GROMACS trajectories. This tool automates complex data processing, generating high-quality plots for molecular biology and drug discovery researchers.

Keywords:
Bash and Zenity computational tool developmentGROMACSHeroMDAnalysisgraphical user interface/automationmolecular dynamic simulation

More Related Videos

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.0K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.6K

Related Experiment Videos

Last Updated: Nov 20, 2025

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

773
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.0K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.6K

Area of Science:

  • Computational Biology
  • Drug Discovery
  • Molecular Modeling

Background:

  • Molecular dynamics simulations (MDS) are crucial in molecular biology and drug discovery.
  • Analyzing MDS trajectories is often complex, manual, and time-consuming.
  • Existing methods can be error-prone for researchers without extensive command-line experience.

Purpose of the Study:

  • To present HeroMDAnalysis, a novel tool for analyzing GROMACS-based MDS trajectories.
  • To automate the generation of high-quality plots for various simulation parameters.
  • To provide an accessible solution for biochemists and synthetic chemists.

Main Methods:

  • Development of an automagical analysis tool using bash shell programming.
  • Integration of a graphical user interface (GUI) built with the Zenity engine.
  • Semiautomated framework for processing and visualizing MDS data.

Main Results:

  • HeroMDAnalysis simplifies complex trajectory analysis tasks.
  • The tool generates high-quality plots efficiently.
  • It significantly reduces the time and effort required for data analysis.

Conclusions:

  • HeroMDAnalysis offers a user-friendly and efficient method for MDS data analysis.
  • The tool empowers researchers with limited command-line experience.
  • It facilitates faster insights in molecular biology and drug discovery research.