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Amber MD Workshop 2011 -- May 3-6, Barcelona

We are glad to announce the Amber Workshop 2011 that will be held in Barcelona from the 3rd to 6th May. The course will be taught by Ross C. Walker and Adrian E. Roitberg and will be hosted by the IRB Barcelona and the Barcelona supercomputing Center.


Classes will be held from Tuesday 3rd to Friday 6th of May, starting at 9:00 AM to 6:00 PM, with breaks for lunch and coffee.

List of covered topics:

  1. Introduction to force fields and molecular dynamics (Lecture)
  2. Overview of AMBER and it's programs (Lecture)
  3. Introduction to setting up and running simulations (Lecture / Hands on)
  4. Visualizing AMBER simulations (Hands on)
  5. Overview of AMBER Force Fiels / Solvent Models etc. (Lecture)
  6. Introduction to implicit solvent and binding energy calculations (Lecture)
  7. Protein folding and advanced analysis (Hands on)
  8. Simulating Sugars and the Glycam Force Field (Lecture / Hands on)
  9. Designing good simulation projects (Lecture)
  10. Dealing with non-standard residues (Lecture / Hands on)
  11. What to do if there is no crystal structure (Lecture)
  12. Statistical mechanics for free energy calculations [Thermodynamic Integration] (Lecture / Hands on)
  13. QM/MM coupled potential simulations (Lecture)
  14. GPU accelerated MD (Lecture)


Attendees consist of Graduate students and postdocs as well as few faculty members interested in learning about Molecular Dynamics techniques.

The number is limited by the availability of hardware for the hands-on tutorials.

These require each student to have access to a desktop running Linux. Student number is limited to 40.


Given the limited number of seats you will be requested to fill a pre-registration form before the 1st of April:

Registration fee is 90 Euros and includes:

  • USB flash drive with training materials
  • Temporal access to remote computing resources
  • Coffee breaks
  • Certificate of attendance


Contact: Meritxell Gavalda
Institute for Research in Biomedicine (IRB Barcelona)

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