Before You Start¶
The GROMACS tutorials in this series are organized by increasing complexity. If you’re completely new to GROMACS, it’s strongly recommended to begin with the first tutorial on a simple bulk-solution-label to get familiar with the software and workflow.
Required Software¶
Each tutorial specifies the minimum required version of GROMACS at the top. While most examples should work with any recent version, using a different version may lead to unexpected errors or differences in behavior or output. When possible, try to match the GROMACS version used in the tutorial when possible.
GROMACS¶
Download and install GROMACS by following the instructions in the GROMACS manual. The installation procedure may vary depending on your operating system (e.g., Linux, macOS, or Windows).
VMD¶
In order to visualize the simulation, install Visual Molecular Dynamics (VMD) [1]. Version 1.9.3 of VMD was used to create the images in this website, but more recent versions should work as well. If you prefer, feel free to use an alternative visualization software.
Python (optional)¶
The version 2.6.1 of MDAnalysis is used together with version 3.11.4 of Python [2, 3]. To plot the results from the simulations, version 3.5.2 of Matplotlib Pyplot is used. All the script used to generate the plots are available from GitHub.
Text editing software¶
To write and edit GROMACS input files, a text editor is required. Any plain text editor will do, such as Gedit, Vim, or Visual Studio Code, Nano, Sublime Text, and Notepad++.
Find the input scripts¶
You can access all the input scripts and data files that are used in these tutorials from GitHub.
Recommended reading¶
To better understand molecular dynamics simulations, I recommend the reading of Understanding Molecular Simulation by Daan Frenkel and Berend Smit [4], as well as Computer Simulation of Liquids by Michael Allen and Dominic Tildesley [5].
To understand the basic concepts of fluid and Soft Matter systems, I recommend reading Basic Concepts for Simple and Complex Liquids by Jean-Louis Barrat and Jean-Pierre Hansen [6], as well as Theory of Simple Liquids: With Applications to Soft Matter by Jean-Pierre Hansen and Ian Ranald McDonald [7].