Before you start

GROMACS tutorials is made of several tutorials that are ordered by increasing difficulty.

Required software

The 2024.2 version of GROMACS is required to follow the tutorials.

GROMACS (2024.2)

Download and install the 2024.2 version of GROMACS by following the instructions of the GROMACS manual. Depending on your operative system (i.e. Linux, macOS, or Windows), the procedure may differ.

VMD (optional)

In order to visualize the simulation, the version 1.9.3 of VMD will be used [1]. Some basic instructions for VMD are given on lammpstutorials, see this link. If you prefer, feel free to use an alternative visualization software like Ovito.

Python (optional)

The version 2.6.1 of MDAnalysis is used together with the version 3.11.4 of Python [2, 3, 4].

To plot the results from the simulations, the version 3.5.2 of Matplotlib Pyplot is used.

Text editing software

To write and edit GROMACS input files, a text editor is required. Any text editor will do, such as gedit, vim, or vscode.

Find the input scripts

You can access all the input scripts and data files that are used in these tutorials from GitHub.