These tutorials are designed as introductory material into using the GROMACS simulation package. GROMACS is free, open-source software, and has consistently been one of the fastest (if not the fastest) molecular dynamics codes available.

There are currently eight tutorials available, with a ninth in the works:

1. Lysozyme in Water: The intent of this tutorial is to give new users a basic introduction into the tools used to prepare, run, and perform simple analysis on a "typical" system with GROMACS.
2. KALP₁₅ in DPPC: This tutorial is more advanced, and is designed for more experienced users who want to simulate membrane proteins and understand force field structure and modification.
3. Protein-Ligand Complex: This tutorial instructs the user on how to deal with a protein-ligand system, with a focus on proper ligand parametrization and topology handling.
4. Free Energy of van der Waals transformation: This tutorial describes the procedure for carrying out a simple free energy calculation, the elimination of van der Waals interactions between a simple molecule (methane) and water. More complicated systems are discussed.
5. Free Energy of Hydration: This tutorial builds upon the methane/water system and includes a full Coulombic and van der Waals transformation for the purpose of calculation ΔG_hydr
6. Binding Free Energy: This tutorial is in development and will guide the user throught the calculation of ΔG_bind for a protein-ligand complex
7. Biphasic Systems: The construction of a biphasic cyclohexane-water system.
8. Umbrella Sampling: Also somewhat advanced, this tutorial is intended for users who wish to learn to use umbrella sampling to calculate the potential of mean force (PMF) along a single, linear degree of freedom.
9. Virtual Sites: This tutorial guides the user through manual construction of virtual sites for a very simple linear, triatomic molecule (CO₂).

All of these tutorials assume you are using GROMACS version 2018 or newer. Some (as noted in the tutorials themselves) require version 2025. If you are using a different version, be forewarned: the tutorials likely will not work as expected.

At the end of each tutorial you will find my contact information if you wish to provide commentary or report anything you find to be incorrect. I genuinely appreciate this kind of feedback, as it helps me design better tutorials and fix things that are not clear (or sometimes wrong, oops). I must ask that you please do not contact me for general GROMACS help or advice on your project. I am continually inundated with help requests and I simply do not have the time to be helpful to everyone.

I hope you find these tutorials useful. If you use these protocols for your research, I ask that you cite the paper that explains the theoretical background of these tutorials:

J.A. Lemkul (2018) "From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package, v1.0" Living J. Comp. Mol. Sci. 1 (1): 5068.
Open-Access Full Text
GitHub

Happy simulating!

For GROMACS installation instructions, refer here.