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Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2015/16



20.1.2016: The Workshop is fully booked! If you are able to fill a last minute cancellation we can put you on the waiting list.

Preparation for the workshop:

  • Please bring your own laptop. We will be in a room that has no workstations. For network access: If you have Eduroam access, you are settled. For the others, we have a number of guest accounts that will grant temporary access to Eduroam at FU-Berlin.
  • Please install PyEMMA - please use the conda environment if possible. See If you have installation problems, please send an email to or There will be a new release just before the workshop, but it's easy to update.


Lecturer: Frank Noé
Assistants: tba
Language: English
SWS:2; LP/Credits: 5
Students: MSc Physics


5-day course 22.-26.2.2016 9:00-15:00 or 9:00-17:00 Arnimallee 6, R. 007/008


In this 1-week compact course (Blockseminar) participants will learn 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 the software package PyEMMA (Emma's Markov Model Algorithms). All computer applications will be done in IPython. We will provide test data, but participants may also bring their own MD data (any standard format, i.e.xtc, dcd) and we will help with applying EMMA to them.
You can use one of our lab PCs or bring your own laptop. In the latter case, FU-Berlin students need to make sure they have Eduroam access. Non-resident students will get a guest account to access Eduroam.

Monday 22: Introduction, featurization, transformation and MSM estimation

  • 9:00-10:30: Introduction and Overview.
  • 11:00-12:30: Coordinate I/O, featurization and transformation, time-lagged independent component analysis (TICA)
  • 13:30-15:00: Markov model estimation validation and discretization error.
  • 15:30-17:00: MSM analysis

Tuesday 23: Coarse-grained kinetic models and Transition path theory.

  • 9:00-10:30: Markov model coarse-graining with PCCA and HMMs
  • 11:00-12:30: Hidden Markov models (HMMs). Comparing HMMs and MSMs
  • 13:30-16:00: Transition Path Theory

Wednesday 24: Free energies and rare-event kinetics

  • 9:00-10:30: Umbrella Sampling, Replica-Exchange, WHAM, MBAR.
  • 11:00-12:30: Tutorials
  • 13:30-16:00: Free energies and Markov models. dTRAM and TRAM.

Thursday 25: Student projects and supervised analysis of your own MD data.

Friday 26: Presentations

All Presentations will be 15 minutes, plus short discussion.

  • 9:00-9:15: Student talk 1 (Grabner, Zais; dimer_1)
  • 9:20-9:35: Maria Kalimeri (U Tampere, Finland) Are thermophilic proteins rigid or flexible?
  • 9:40-9:55: Student talk 2 (Dovhopolyi, Wille; re-estimation)
  • 10:00-10:15: N. Verma (U Düsseldorf, Germany) A study of conformational dynamics of the steric chaperone lipase foldase by MD simulations with MSM and FRET
  • 10:20-10:35: Coffee Break
  • 10:40-10:55: Student talk 3 (Natemeyer, Paßler; maze)
  • 11:00-11:15: Justin Chen (Rice University, USA) Theoretical Predictions using limited experimental data
  • 11:20-11:35 Student talk 4 (Gorriz, Volkenandt; tpt)
  • 11:40-11:55 Student talk 5 (Manni, Tegtmeier; dimer_2)

  • 13:00-13:15 Student talk 6 (Gutjahr, Haselsteiner, van der Bosch; umbrella_sampling)
  • 13:20-13:35 Giray Enkavi (U Tampere, Finland) NPC2-Mediated Cholesterol Trafficking
  • 13:40-13:55 Student talk 7 (Deecke, Lee; hmm)
  • 14:00-14:15 Coffee Break
  • 14:20-14:35 Student talk 8 (Crovetto, Elsayed; multi_temperature)
  • 14:40-14:55 Oleksandra Kukharenko (U Konstanz, Germany) Analysis of the simulation data of intrinsically disordered peptide
  • 15:00-15:15 Alex Kluber (Rice University, USA) Does topology determine the sensitivity to frustration in protein folding?

Credit Requirements (Scheinkriterien)

  • Active participation: Students will get project assignments (2 students per project) on wednesday, will work it out on thursday, and will present it on friday (15 mins, both students should present).
  • For physics students, this course counts as a Seminar "Selected Topics in Physics" (5 LP)
  • All participants will receive a certificate of attendance.
  • Non resident students of i.e. HU or TU, please inform us prior to the workshop if you need a "Schein".


Name Consultation Hour Mail
Frank Noé appointment by email. Arnimallee 6, R213 frank.noe[at]
Katja Geiger registration non-resident students katja.geiger[at]

Information for non-resident participants


For directions and area map see here.


Freie Universität does not operate on-campus guest houses or student dormitories. Therefore, participants from outside of Berlin must arrange their own accomodation. A good budget choice near campus is Residenz 2000 Aparthotel. For more links see the official accommodation listing.


Note that the workshop takes place during term break and the student cafeteria will be closed. please bring your own soft drinks and snacks as we can only provide coffee, tea and mineral water. For lunch there are several options within walking distance.

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