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Welcome to the Computer Tutorial in Markov Modeling WS 2014/15


Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is required.
If you have problems registering, contact katja.geiger[at]


Lecturer: Frank Noé
Assistants: Martin Scherer, Benjamin Trendelkamp-Schroer, Fabian Paul
Language: English
SWS:2; LP/Credits: 5
Students: MSc Physics; MSc Mathematics


5-day course 23 to 27 February 2015 9:00-15:00 Arnimallee 6 room 030 (PC pool)


In this 1-week compact course (Blockseminar) participants will be taught how to construct Markov models for molecular dynamics simulation data and how to analyze them quantitatively. The course will take place in a computer lab and will include both theory lessons (20-30%) as well as practical applications using data. Applications will be done with the software package EMMA. We will provide test data, but participants may also bring their own MD data and we will help with applying EMMA to them.

  • Theory: discretization and discretization error, transition path theory
  • Computer applications: EMMA (Emma's Markov Model Algorithms), including installation and application to model data
  • All computer applications will be done in python / iPython.
  • You can use one of our lab PCs or bring your own laptop. In the latter case, make sure you have Eduroam access.

Credit Requirements (Scheinkriterien)

  • Active participation, including a short presentation of a 1-day task.
  • For physics students, this course counts as a Seminar "Selected Topics in Physics" (5 LP)
  • For mathematics students, this course counts as a "Forschungsseminar" (5 LP)


Name Consultation Hour Mail
Frank Noé appointment by email. Arnimallee 6, R213 frank.noe[at]
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