Programme

Final Agenda:

10 Nov 2016 – Thursday Morning (CET time)

08:00-08:30 Registration and posters set up
08:30-09:00 Setting up AWS for attendees
09:00-09:15 Session 1a: Introduction and what’s new by G. De Fabritiis
09:15-10:10 Session 1b: Python primer and HTMD molecules by J. M. Damas [Download tutorial notebooks]
10:10-10:30 Coffee break
10:30-11:40 Session 2: Working with molecules and projections by J. M. Damas [Download tutorial notebooks]
11:40-12:00 Coffee break
12:00-13:10 Session 3: Protein preparation, protonation and building by T. Giorgino [Download tutorial notebooks]
13:10-14:00 Lunch

10 Nov 2016 – Thursday Afternoon (CET time)

14:00-15:10 Session 4: Talks
-Shozeb Haider: DNA building in HTMD. [Download tutorial notebooks]
-Adrià Pérez: Allosteric mutual information detection.
15:10-15:40 Coffee break
15:40-16:15 Session 5a: MD protocols in HTMD by G. De Fabritiis [Download tutorial notebooks]
16:15-16:50 Session 5b: Introduction to AceCloud by M. Harvey [Download tutorial notebooks]
16:50-17:20 Coffee break
17:20-18:30 Session 6: Small molecule parameterisation with HTMD by M. J. Harvey [Download tutorial notebooks]
Using PLUMED2 Metrics by T. Giorgino [Download tutorial notebooks]
18:30-20:30 Poster session

11 Nov 2016 – Friday Morning (CET time)

09:00-10:10 Session 7: Talks
-Guillermo Pérez Hernández: Analysis of MD simulations via Markov State Models: an introduction.
-Esam Abualrous: Molecular mechanism of T cell receptors binding to MHC class II proteins: High-throughput molecular dynamics simulation and Markov modeling.
10:10-10:30 Coffee break
10:30-11:40 Session 8: Markov State Model Analysis in HTMD by S. Doerr [Download tutorial notebooks]
11:40-12:00 Coffee break
12:00-13:10 Session 9: New Adaptive Sampling Method in HTMD by S. Doerr [Download tutorial notebooks]
13:10-14:00 Lunch

11 Nov 2016 – Friday Afternoon (CET time)

14:00-15:10 Session 10: Hands-on: Mini project on membrane permeation [Download tutorial notebooks]
15:10-15:40 Coffee break
15:40-16:50 Session 11: Talks
-Anna Duncan: Organisation of potassium channels in complex membranes via coarse-grain MD simulations.
-Juan C. Mobarec: Molecular Dynamics Simulations of Class B G Protein-Coupled Receptors.
-Robert Weinzierl: MD Simulation of Activation Domain – Coactivator Interactions.
16:50-17:20 Coffee break
17:20-18:30 Session 12: Working on your projects* (dev or data analysis)
18:30-19:00 Final discussion and closing
20:30- Social dinner & tour of the best bars in Barcelona

There will be four types of sessions, with ample time for discussion after each one:

  • Talks to highlight some of the topics.
  • Poster presentations.
  • Hands-on sessions to test your systems. You will need to bring with your own PC. We highly recommend using Linux or Mac OS operating system. SSH and Chrome must be installed on all laptops. For laptops using Windows OS, please install also putty.
  • *Working on your projects. You can bring your own system file. To optimize the support given to each participant, please, send us a brief description of your system (e.g. pdb reference, number of atoms in the system, system with membrane…) and describe the development you are interested in (file preparation, analysis…) Important: Your data files must be readily downloaded on your own laptop.