Category:Tutorials

From wiki.gromacs.org

Documentation and resources for assisting those in learning the use of GROMACS.

Contents 1 Resources 1.1 General 1.2 Free Energy Calculations 1.3 Membrane Simulations 1.4 QM/MM 1.5 Development

[edit] Resources

[edit] General

• step-by-step demo and several simple examples are available in the share/tutor subdirectory of your GROMACS installation.
• Introduction to Molecular Dynamics.
• MD for drug design (GROMACS) - (Daan van Aalten).
• GROMACS introductory tutorial - solvation study of spider toxin peptide (John E. Kerrigan).
• GROMACS tutorial for drug – enzyme complex solvation - (John E. Kerrigan).
• 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, confirmational 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.

[edit] Free Energy Calculations

• Introduction to free energy calculation methods - (Gilles Pieffet, Alan E. Mark ).

[edit] Membrane Simulations

• 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.

[edit] QM/MM

• QM/MM calculations on a Diels-Alder antibody catalyst - study a catalytic antibody that catalyzes the Diels Alder cyclo-addition reaction

[edit] Development

• Patching mdrun a simple example