Documentation and resources for assisting those in learning to use GROMACS.
Workshops and Teaching Materials
- GROMACS Workshop 2007 - lectures by GROMACS developers, contributed talks by participants and hands on workshops. Talks available as PDF and video files. Workshop files available.
- Molecular Dynamics Simulations for Biomolecules with GROMACS 3 2004 - course focused on molecular dynamics simulation methods in studying large biomolecules. Lectures covered both overall methods and more detailed theoretical background of MD simulations of biomolecules. Talks available as PDF and video files.
- EMBO04: Methods for protein simulations and drug design - series of lectures and practicles covering: molecular dynamic simulation with GROMACS, molecular dynamics for drug design, membrane protein simulations, normal mode analysis, conformational analysis, docking and scoring, flexible docking and hybrid QM/MM. Talks available as PPT slides and WMV video files. Practicals available, including the starting files.
General GROMACS Use
- A step-by-step demo and several simple examples are available in the share/tutor subdirectory of your GROMACS installation.
- 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).
- GROMACS introductory tutorial - solvation study of spider toxin peptide (John E. Kerrigan).
- GROMACS introductory tutorial in Portuguese (Brazil) - Introdução ao GROMACS e dinâmica molecular em português (BR) / Introduction to GROMACS and molecular dynamics in Portuguese (BR) - Ricardo O.S. Soares.
- Another lysozyme tutorial - focused on details of the topology and explaining the ins and outs of each preparation step, designed for GROMACS 4.5.x (Justin A. Lemkul)
- MD for drug design (GROMACS) - (Daan van Aalten).
- GROMACS tutorial for drug – enzyme complex solvation - (John E. Kerrigan).
- 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
- Insertion of methane in water - David Mobley
- Simple free energy calculations - an updated version of the Mobley tutorial using BAR and discussing a few other topics, for use with GROMACS 4.5.x (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)
- GROMACS tutorial for membrane protein simulations - designed to demonstrate what sorts of questions and problems occur when simulating proteins that are embedded within a lipid bilayer.
- 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
Pull Code and Umbrella Sampling
- Using umbrella sampling to calculate the potential of mean force - how to use the pull code of GROMACS 4 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)