Setting up protein simulations

This workshop was an updated version of our previously run How to set up a protein simulation course and was run by Dr Charlie Laughton (University of Nottingham) and Dr Syma Khalid (University of Southampton). The workshop focussed on the three main challenges of setting up a simulation:

1. preparing your protein for simulations, to include: missing atoms/residues; protonation states; unusual geometries etc
2. adding ions and solvent, to include: which ions to use; ion placement; solvent types etc
3. equilibration and simulation, to include: equilibration set-ups for different types of system; information on differing simulation strategies

The principles for these challenges are the same whatever simulation software is used, however during the hands-on sessions at the workshop delegates had a choice of following AMBER or GROMACS orientated tracks.

Documentation from the course is available for download.

Session 1 - preparing your protein (presentation, tutorial, additional tutorial notes)
Session 2 - adding ions and solvent (presentation, AMBER tutorial, GROMACS tutorial)
Session 3 - equilibration (presentation, AMBER tutorial, GROMACS tutorial)

All files for the practical session are available as a compressed tar file here (100MB).