HPC @UPV/EHU

AMBER is a family of force fields and programs for molecular dynamics of biomolecules. 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.

AMBER MD Workshop 2011

May 3-6, Barcelona.
Limited number of seats. You will be requested to fill a pre-registration form before the 1st of April.
Workshop web page.
AMBER web page

Program

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 Fields / 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).

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