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

Abstract

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 articlepresents a project calledHeroMDAnalysis, an automagical tool to analyze the GROMACS-based MDS trajectories and generate plots as high-quality images for various parameters. Materials &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 acomplex, manual, time-consuming and error-prone task, presenting a useful method forbiochemists and synthetic chemists with no prior experience of the command line interface.