Scalable Software Services for Life Science

Tutorials

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

 

Protein-Ligand Systems

 

Free Energy Calculations

 

Membrane Simulations

 

Heterogeneous Systems

 

QM/MM

 

Pull Code and Umbrella Sampling

 

Virtual Sites

 

Development

  1. 1. Workshops and Teaching Materials
  2. 2. General GROMACS Use
  3. 3. Protein-Ligand Systems
  4. 4. Free Energy Calculations
  5. 5. Membrane Simulations
  6. 6. Heterogeneous Systems
  7. 7. QM/MM
  8. 8. Pull Code and Umbrella Sampling
  9. 9. Virtual Sites
  10. 10. Development