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GROMACS tutorials: overview

Note

The GROMACS tutorials that follow were written in Markdown by Wes Barnett and were originally published in the tutorials section of his former website. The tutorials are presently maintained by Vedran Miletić and published in the tutorials section of the Group for Applications and Services on Exascale Research Infrastructure (GASERI) website.

These are some GROMACS tutorials for beginners that I wrote during my Ph.D. work. I found that many GROMACS tutorials focused on biomolecules such as proteins, where few focused on simple systems. I hope these tutorials fill the gap and give you a greater understanding of how to set up and run simple molecular simulations and how to utilize advanced sampling techniques.

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 the 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 (e.g., bash). Specifically, you should know how to make directories, change your current directory into them, edit text files, and download files to your system. When you see a $ or > this is the prompt on the command line and indicates you should type the text following it. If the command line is new to you, consider searching for a 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. Window sampling -- How to get methane-methane PMF from window sampling using pull code.
  6. Test particle insertion -- How to get the excess chemical potential of methane using test particle insertion.

Questions?

See my contact page.

Author: Wes Barnett, Vedran Miletić