GROMACS Tutorials

Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry

All tutorials have been updated for GROMACS version 2018!

Tutorial 1: Lysozyme in Water

Tutorial 2: KALP15 in DPPC

Tutorial 3: Umbrella Sampling

Tutorial 4: Biphasic Systems

Tutorial 5: Protein-Ligand Complex

Tutorial 6: Free Energy of Solvation

   
 

Tutorial 7: Virtual Sites

 

These tutorials are designed as introductory material into using the GROMACS simulation package. GROMACS is free, 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. Lysozyme in Water: The intent of this tutorial is to give new users a basic introduction into the tools used to prepare, run, and perform simple analysis on a "typical" system with GROMACS.
  2. KALP15 in DPPC: This 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. Umbrella Sampling: Also somewhat advanced, this tutorial is intended for users who wish to learn to use umbrella sampling to calculate the potential of mean force (PMF) along a single, linear degree of freedom.
  4. Biphasic Systems: The construction of a biphasic cyclohexane-water system.
  5. Protein-Ligand Complex: The fifth tutorial instructs the user on how to deal with a protein-ligand system, with a focus on proper ligand parametrization and topology handling.
  6. Free Energy of Solvation: This 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. Virtual Sites: This tutorial guides the user through manual construction of virtual sites for a very simple linear, triatomic molecule (CO2).

All of these tutorials assume you are using GROMACS version 2018 or newer. 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 between versions, especially with new features introduced in versions 5.0 and 5.1, and even some changes since the 2016.x series. 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 please do not contact me for general GROMACS help or advice on your project. I am continually inundated with help requests and I simply do not have the time to be helpful to everyone.

I hope you find these tutorials useful. If you use these protocols for your research, I ask that you cite the paper that explains the theoretical background of these tutorials:

J.A. Lemkul (2018) "From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package, v1.0" Living J. Comp. Mol. Sci. In Press. GitHub

Happy simulating!

For GROMACS installation instructions, refer here.

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