We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein, and a complex. In this article, we will analyze the GROMACS [1] output of MD simulation of a complex.Contents 1. RMSD2. RMSF3. Radius of gyration4. Hydrogen bondsProtein-ligand interactionsReferencesFurther Reading We … Continue reading Tutorial: MD simulation output analysis of a complex using GROMACS