GROMACS Tutorials

These are some GROMACS tutorials for beginners. It’s not necessary to do the tutorials in order, but the first two tutorials are essential before going on to the others, as the structure file (methane.pdb) and topology file (topol.top) for methane from tutorial 2 are used in all subsequent tutorials. The tutorials are designed for GROMACS version 5.1 and up. If you are using an older version, some of the commands or parameters may have changed. Note especially that the pull code for umbrella sampling has changed since 5.0 and older releases.

Prerequisites

I assume you have some working knowledge of the command line. Specifically, you should know how to make directories, change into them, edit text files, and download files to your system. When you see a $ or > this is the prompt on the commandline and indicates you should type the text following it. If the commandline is new to you, consider going through CodeAcademy’s tutorial.

I also assume you have GROMACS installed on a machine available to you. Source code and installation instructions can be found on the GROMACS documentation page.

Throughout the tutorials we’ll be using OPLS methane and TIP4PEW water.

Contents

  1. Water - Basics of setting up a simulation. Find out the density of TIP4PEW water.
  2. One methane in water - How to create a topology file for a molecule and solvate it. Get the radial distribution function.
  3. Several methanes in water - How to put multiple solutes into a system. Get the methane-methane potential of mean force.
  4. Free energy of solvation of methane - How to do a free energy simulation when coupling a molecule. Use MBAR to get the result.
  5. Umbrella sampling - Get methane-methane PMF from umbrella sampling using pull code.
  6. Test particle insertion - Get the excess chemical potential of methane using test particle insertion.

Issues

If there is an error or mistake in a tutorial, or if something is unclear, please open an issue, and I will be happy to address it. If you have a general question about GROMACS see the GROMACS documentation. You can also direct general questions about GROMACS to their mailing list.