Welcome to the GROMACS tutorials!

This is the home of the free online GROMACS tutorials. The tutorials are provided as interactive Jupyter notebooks. This is the same content regularly used in training workshops around GROMACS. You can download the notebooks to run on your own computer, or run them right now in your browser, thanks to mybinder.org.

Jupyter notebooks are a popular way to provide online interactive computational content. If they are new for you, then perhaps you would like to check out a quick Youtube video. Or in alternative have a look at the learning pathway: Using Jupyter Notebooks for biomolecular research.

Available tutorials

• Introduction to Molecular Dynamics

• Introduction to Membrane-Protein Simulation

• Umbrella sampling

• Free energy of solvation

• Potential of mean force using AWH method

• Free energy of solvation using AWH method

Licensing

All the GROMACS tutorials available from this site are freely licensed under the CC-BY-4.0 You are welcome to use them in any way, download them for personal use or use in your own teaching. Please acknowledge the funding agencies who supported this work and the people who developed the content.

Other GROMACS training resources

• Justin Lemkul’s GROMACS tutorials: http://www.mdtutorials.com/gmx/

• GROMACS tutorials by Wes Barnett and Vedran Miletić: https://group.miletic.net/en/tutorials/gromacs/

• Mapping computation to HPC hardware & GPU accelerators and heterogeneous architectures by Szilárd Páll and Berk Hess https://doi.org/10.6084/m9.figshare.22303477

• GROMACS GPU performance by Mark Abraham: https://enccs.github.io/gromacs-gpu-performance/

• GROMACS-CP2K QMMM tutorial by Dmitry Morozov: https://github.com/bioexcel/gromacs-2022-cp2k-tutorial