GROMACS Tutorials

Justin A. Lemkul, Ph.D.

Department of Pharmaceutical Sciences
University of Maryland, Baltimore

Formerly of the Department of Biochemistry, Virginia Tech

Tutorial 1: Lysozyme in Water
Updated for 5.0
Tutorial 2: KALP15 in DPPC
Updated for 5.0
Tutorial 3: Umbrella Sampling
Tutorial 4: Biphasic Systems
Updated for 5.0
Tutorial 5: Protein-Ligand Complex
Updated for 5.0
Tutorial 6: Free Energy Calculations
   
  Tutorial 7: Virtual Sites
Updated for 5.0
 

These tutorials are designed as introductory material into using the GROMACS simulation package. GROMACS is open-source software, and has consistently been one of the fastest (if not the fastest) molecular dynamics codes available.

There are currently seven tutorials available:

  1. The first is a simple system, lysozyme in water with ions. Its intent is to give new users a basic introduction into the tools used to prepare, run, and analyze a typical system with GROMACS.
  2. The second tutorial is more advanced, and is designed for more experienced users who want to simulate membrane proteins and understand force field structure and modification.
  3. The third is also somewhat advanced, intended for users who wish to learn to use umbrella sampling to calculate the potential of mean force (PMF) along a single degree of freedom.
  4. The fourth tutorial guides the user through the construction of a biphasic cyclohexane-water system.
  5. The fifth tutorial instructs the user on how to deal with a protein-ligand system, with a focus on proper ligand parameterization and topology handling.
  6. The sixth tutorial describes the procedure for carrying out a simple free energy calculation, the elimination of van der Waals interactions between a simple molecule (methane) and water. More complicated systems are discussed.
  7. The seventh tutorial guides the user through manual construction of virtual sites for a very simple linear molecule (CO2).

Various other tutorials are in development and will be posted as they are ready.

Most of these tutorials assume you are using version 4.5.3 of GROMACS or newer, and all are currently being upgraded such that a minimum version of 5.0 will be required. If you are using an older version, not all of the features detailed here will work! Some of the .mdp options and command line arguments change substantially between versions, especially with the move to 5.0. Each tutorial states which version it expects you are using. If you are using a different version, be forewarned: the tutorials likely will not work as expected.

At the end of each tutorial you will find my contact information in order to provide commentary or report anything you find to be incorrect. I genuinely appreciate this kind of feedback, as it helps me design better tutorials and fix things that are not clear (or sometimes wrong, oops). I must ask that you do not contact me for general GROMACS help, advice on your project, or any other purpose. I provide these tutorials as a service to the GROMACS community, without warranty or guarantee of technical support. I am continually inundated with help requests and I simply do not have the time to be helpful to everyone. I already deal with enough email :)

I hope you find these tutorials useful. Enjoy!

For GROMACS installation instructions, refer here.



These tutorials were originally written while I was a member of Dr. David Bevan's research group at Virginia Tech.

Bevan Lab Homepage

Virginia Tech Homepage

Virginia Tech Biochemistry


Site design and content copyright 2008-2014 by Justin Lemkul
These materials are provided free of charge for use by anyone for the purpose of learning to use the GROMACS software.
Reproduction, redistribution, or other publication of the content of any of these tutorials in any medium without written permission of the author is prohibited.
Use in classroom teaching environments solely for the purpose of education is permitted.
Problems with the site? Send them to the Webmaster