Gromacs

Tutorials

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

     

    Workshops and Teaching Materials

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

     

    Protein-Ligand Systems

     

    Free Energy Calculations

     

    Membrane Simulations

     

    Heterogeneous Systems

     

    QM/MM

     

    Pull Code and Umbrella Sampling

     

    Virtual Sites

     

    Development

    Page last modified 18:57, 7 Sep 2013 by mrshirts?