ASGARD. A simple and automatic GROMACS tool to analyze Molecular Dynamic simulations

One of the most popular techniques for analyzing the physical movement of molecules is molecular dynamics (MD) simulations. Among the different programs used to perform them, GROMACS is one of the most widely used open-source packages. We present ASGARD, a software tool for performing analysis of MD protein or protein-ligand complex simulations and generating the corresponding report via an automated MD workflow. After completing the simulation, this tool automatically generates a set of analyses, including reports about overall system stability and system flexibility analysis with RMSD Fluctuation and Distribution calculations. Finally, a dynamic analysis with SASA and DSSP method graphs and different interaction analyses are performed. In conclusion, ASGARD allows the user to run MD simulation analysis with a single command line instead of using several GROMACS programs for each analysis and analyze their result individually. Following this, it automatically creates an analysis report, which helps to understand the molecular interactions and structural changes.

The ASGARD tool generated these data files (xvg, png, and PDF report files). Also, the output files generated by GROMACS MD (trajectory files, topology files, and other types of files) used as the input folder in the three cases are uploaded.