Past Events

How to set up a Protein Simulation, 3rd edition
Monday 29 September 2014

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


Donald Broadbent Lab, Department of Experimental Psychology, Tinbergen Building, 9 South Parks Road, Oxford, OX1 3UD


Syma Khalid (Southampton)
Phill Stansfeld (Oxford)

The workshop will be focussed on the three main challenges of setting up a simulation:

  • Preparing your protein for simulations, to include: missing atoms/residues; protonation states; unusual geometries.
  • Adding ions and solvent, to include: which ions to use; ion placement; solvent types etc.
  • Equilibration and simulation, to include: strategies for checking the system has relaxed and set-ups for different types of system.

It will also cover 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/second year PhD students.

The one-day workshop is likely to start at 10am and be finished by 5pm. A more detailed programme will be available soon.

Registration - deadline 14th September

There is no registration fee for this workshop. However, participants are responsible for their own travel and accommodation costs. The course is restricted to 30 participants.

Please register your interest here. The deadline for applications is the end of Sunday 14th September. If the course is over-subscribed, we will select candidates based on location and experience, in order to maximise the impact of the course. Applicants will be notified as soon as possible as to whether they have a place, and not later than Friday 19th September.


Although we do not provide accommodation for this workshop we would recommend the following sites for anyone that requires an overnight stay.

All delegates are responsible for making their own bookings.