Past Events

How to set up a Protein Simulation, 1st edition
Friday 20 April 2012

This workshop is aimed at beginners wishing to learn the practicalities of setting up a protein molecular dynamics simulation.

Instructors: Syma Khalid (Southampton) and Peter Bond (Cambridge)

The one-day workshop is likely to start at 10.00 and finish by 1700. A more detailed programme will be available soon. The workshop will be 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.
  2. Adding ions and solvent, to include: which ions to use; ion placement; solvent types etc.
  3. Equilibration and simulation, to include: strategies for checking the system has relaxed and set-ups for different types of system.
  4. Basic analysis techniques.

The principles for these challenges are the same whatever simulation software is used, however during the hands-on sessions the workshop will focus on the GROMACS simulation package. Some knowledge of the Linux operating system is desirable, but not essential.

The workshop is aimed at, although not restricted to first and second year PhD students. There is no charge for the workshop, although there are only 16 places available, so we recommend early registration to avoid disappointment. Priority will be given to UK students. Some travel bursaries may be available to help with costs.