Dear colleagues,
we are organizing a tutorial on Markov modeling and free energy calculations from molecular dynamics (MD) data. In the course, we will teach how to use the PyEMMA software (http://pyemma.org) for this purpose. Topics include:
- Featurization of MD trajectories
- Markov state modeling and Hidden Markov modeling
- Dynamical dimension reduction (TICA, VAMPnets)
- Transition path theory (TPT)
- Free energy and rare event kinetics calculation from multi-ensemble data (WHAM, TRAM, Umbrella sampling, replica-exchange)
The course is free of charge. You will need to bring your laptop and have PyEMMA installed. The core course consists of the first three days of lectures and tutorials. Days 4-5 are optional - on these days participants can work on their own projects under our guidance and there will be research talks by the participants:
3-day core course (lectures + tutorials): February 19.-21., 2018
5-day extended course (+ project day + talks): February 19.-23., 2018
For detailed information, see:
http://www.mi.fu-berlin.de/w/CompMolBio/EmmaSeminar17_18
Please send registrations to
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If you are interested to give a short research talk, indicate this in the email and give a title+abstract.
Best,
Frank Noe.
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