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Workshop Timetable
Day 1 - Fri 23rd Oct
- 9.00 Arrive
- 9.30 - 10.30 Lectures
- 10.30 - 11.00 Coffee Break
- 11.00 - 12.30 Practical - Running ExTASY workflows on ARCHER (IB)
- 12.30 - 13.30 Lunch
- 13.30 - 15.00 Practical - Using and extending ExTASY workflows (AS)
- Tutorial on CoCo/Amber followed by...
- the hybrid combination of custom generated kernels with ExTASY available ones, as examples to extend ExTASY. The gromacs/coco workflow will be showcased for this purpose.
- Tutorial on LSDMap / DM-d-MD is also available for those who are interested
- 15.00 - 15.30 Coffee Break
- 15.30 - 17.00 Practical - Sampling other systems with ExTASY (AS)
- 17.00 Finish
Day 2 - Sat 24th Oct
- 9:30 - 10:30 Lectures: Introduction to Markov state modeling and PyEMMA (www.pyemma.org)
- 10:30 - 11:00 Coffee break
- 11:00 - 12:30 Practical - Reading MD data, Featurizing, time-lagged indpendent component analysis (TICA) and Clustering
- 12:30 - 13:30 Lunch
- 13:30 - 15:00 Practical - Markov state model estimation and analysis
- 15:00 - 15:30 Coffee breach
- 15:30 - 17:00 Practical - Coarse-graining of Markov state models, Hidden Markov models and Transition path theory (TPT)
- 17:00 Finish
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