GROMACS tutorial: Introduction to Molecular Dynamics

Here we learn step-by-step how to run a molecular dynamics simulation of a small protein in water solution using GROMACS. We will go through both how to set up the input files, as well as how to set up energy minimization and simulations at constant temperature and at constant pressure. Finally we briefly introduce some of the GROMACS tools for analyzing molecular simulation trajectories.

The tutorial is provided as an interactive Jupyter notebook based on GROMACS. You can run the tutorial online in your browser without installing anything, or download it to run locally with your own installed software.

https://tutorials.gromacs.org/md-intro-tutorial.html