This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general use.

This tutorial assumes you are using a GROMACS version in the 2025.x series. It was prepared and tested with version 2025.2.

Looking for the older (2018) version of this tutorial? You can find it here.