Tutorials

Documentation and resources for assisting those in learning to use GROMACS.

GROMACS USA Workshop and Conference 2013 - Tutorials presented at the 2013 Workshop at the University of Virginia, Charlottesville, VA, USA, September 13th-15th, 2013

Introduction to Molecular Dynamics (Tsjerk A. Wassenaar and Alan E. Mark).
Introduction to Molecular Dynamics Simulations and Analysis - Tutorial for performing and analyzing simulations of proteins. Includes examples of many of the gromacs analysis tools and addresses a number of issues that are commonly raised on the GROMACS user list. This tutorial uses GROMACS version 3.3.1 (Tsjerk A. Wassenaar).
Another lysozyme tutorial - focused on details of the topology and explaining the ins and outs of each preparation step, designed for GROMACS 2018 (Justin A. Lemkul)

Protein-ligand complex (T4 lysozyme) - an example of a protein-ligand/drug system, with focus on proper topology handling and parameterization methodology (Justin A. Lemkul)

Hydration of toluene and transformation to p-cresol - Gilles Pieffet, Alan E. Mark
Simple free energy calculations - an updated version of the Mobley tutorial using BAR and discussing a few other topics, for use with GROMACS 2018 (Justin A. Lemkul)
Another tutorial for calculating a free energy of solvation by Sander Pronk. This one focuses on the role of such calculations in a ligand binding free energy calculation (which is a little too expensive to do in a workshop setting).

Detailed instructions on topology organization and system construction - building a KALP-15/DPPC system, with step-by-step instructions for topology organization, tips, and troubleshooting (Justin A. Lemkul)
GPCR simulation - based on Justin's KALP-15 tutorial, Anirban Ghosh describes a procedure for simulating GPCRs

Building biphasic systems - a cyclohexane/water layer system, with tips for protein insertion (Justin A. Lemkul)

QM/MM calculations on a Diels-Alder antibody catalyst - study a catalytic antibody that catalyzes the Diels Alder cyclo-addition reaction
QM/MM calculations on thymine dimer repair - study the spontaneous splitting of a thymine dimer in DNA

Using umbrella sampling to calculate the potential of mean force - how to use the pull code of GROMACS 2018 to run umbrella sampling simulations (Justin A. Lemkul)

Using virtual sites to create a linear molecule - a simple example of building CO₂ with virtual sites, focusing on the construction of the topology and verification of moments of inertia (Justin A. Lemkul)

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