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

Background & objective: Molecular dynamics simulations (MDS) using GROMACS are among the commonly used computational experiments in the area of molecular biology and drug discovery. This article presents a project called HeroMDAnalysis, an automagical tool to analyze the GROMACS-based MDS trajectories and generate plots as high-quality images for various parameters. Material & methods: The tool was built using bash shell programming, and graphical user interface was built using Zenity engine. Results & conclusion: This tool offers a simple, semiautomated, and relatively fast framework for what was previously a complex, manual, time-consuming and error-prone task, presenting a useful method for biochemists and synthetic chemists with no prior experience of the command line interface.

Automated summary

The article introduces an automated tool called HeroMDAnalysis for analyzing GROMACS-based MDS trajectories and generating high-quality images. The tool is simple, semi-automated, and relatively fast, providing a useful method for biochemists and synthetic chemists without command line interface experience.