Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
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:
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. 1 (1): 5068.
For GROMACS installation instructions, refer here.
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The contents of all tutorials on this site are made available under the CC-BY 4.0 license
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