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Welcome to the Computer Tutorial in Markov Modeling (PyEMMA) WS 2016/17



For those who were not able to attend the workshop see here:
Link to notebooks
Link to youtube playlist

27.2.: Students not in Campus Managment please do a "Modulanmeldung". Use the form on the Registrar's office website. Complete and drop into mail box outside of registrar's office.
22.2.: All participants will receive a Certificate by email after the workshop. Students from other unis will in addition get a paper certificate (Schein) stating their credits after the Friday presentations
19.2.: On Monday, we will be there from 8 am. For registration you only need to sign the participants' list at the registration desk. After arrival please check if you have wifi access.
18.2.: For directions to workshop see How to find us


5-day course 20.-24.2.2017 9:00-15:00 Takustr. 9, r.005 (ground floor)


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 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 Jupyter Notebooks (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 PyEMMA to them.
Please bring your own laptop. Participants without Eduroam access will get a temporary login for the campus wifi.



Mon Tue Wed Thu Fr
09-12 lectures/tutorials lectures/tutorials lectures tutorials contributed talks projects
12-13 lunch break lunch break lunch break lunch break lunch break
13-15 lectures/tutorials lectures/tutorials lectures/tutorials projects* student talks

*On Thursday afternoon, assistants will be available until 17h to assist with projects.


Monday, 20 Feb

09:00-10:00 Introduction and Markov State Model (MSM) primer
10:00-10:30 PyEMMA overview
10:30-12:00 I/O, featurization, time-lagged independent component analysis (TICA), variational principle
12:00-13:00 Lunch break
13:00-14:00 MSM estimation
14:00-15:00 advanced MSM estimation

Tuesday, 21 Feb

09:00-10:00 MSM theory
10:00-10:30 Visualisation - Interactive Projection Explorer
10:30-11:15 MSM analysis
11:15-12:00 MSM coarse graining
12:00-13:00 Lunch break
13:00-15:00 Comparing Hidden Markov models (HMM) and MSM

Wednesday, 22 Feb

09:00-10:30 Enhanced Sampling
10:30-12:00 Multi-ensemble Markov Models (MEMMs)
12:00-13:00 Lunch break
13:00-15:00 MEMM Hands-on

Thursday, 23 Feb

Time Speaker Title
9:00 Andrea Cesari (SISSA, Trieste) Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement
9:20 Sabine Reißer (SISSA Trieste) Combining molecular dynamics and NMR spectroscopy to characterize structure and dynamics of an RNA hairpin from an inverted SINEB2
9:40 Javier Iglesias-Fernández
and Sílvia Osuna (Univ. Girona)
Microsecond Molecular Dynamics of natural and evolved stand-alone LovD enzyme variants
10:00 Barira Islam and Petr Stadlbauer (CEITEC) Insights into conformational dynamics and folding of G-quadruplexes using MD simulations
10:20 Raquel Romero (UCL) Computational studies of Glucocerebrosidase in complex with its activator protein Saposin-C
10:40 Nuria Plattner (FUB) Markov state models for protein domain interactions and protein-ligand binding
11:00 Simon Olsson (FUB) Some links between experimental data and Markov models
11:20 Giovanni Pinamonti (FUB) Studying the kinetic properties of small RNA molecules using Markov state models
11:40 Sebastian Stolzenberg (FUB) MHC class II complexes sample intermediate states along the peptide exchange pathway
12:00-13:00   Lunch break
13:00-15:00   Projects*

*assistants will be available until 17h to assist with projects.

Preparation for course

Installation of PyEmma

For tutorials, we will use the Python-based software package PyEMMA (Emma's Markov Model Algorithms,, We strongly recommend to install PyEMMA from the anaconda Python distribution via conda install -c omnia pyemma
If you are not using the anaconda Python distribution, PyEMMA is also available via source installation from github. For more detailed installation instructions, please refer to
If possible, install the latest release of PyEMMA. For troubleshooting contact christoph.wehmeyer[at]

Wifi Access

Please check your wifi access after arrival at the institute.
For wifi access select network ‘eduroam’ (not ‘conference’)
If your home institute supports eduroam, log in with username and home domain (i.e.
Participants without eduroam access can pick up a guest account (username & password) at the registration desk. Log into the ‘eduroam’ network with Please sign the guest account list with your name + DOB (required for some reason).

Materials and Videos

For those who were not able to attend the workshop see here:
Link to notebooks
Link to youtube playlist

Information for local students


Language: English
SWS:2; LP/Credits: 5

Credit Requirements (Scheinkriterien)

  • Active participation: Students will get project assignments (usually 2 students per project) on Wednesday, will work on the project on Thursday afternoon and Friday morning, and present it on Friday afternoon (15 mins per team, 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, i.e., HU or TU, please inform us prior to the workshop if you need a "Schein".

Information for participants from outside of Berlin

How to find us

The workshop takes place at Freie Universität, Institute of Computer Science, Takustr. 9, 14195 Berlin
Important: Although the official address is Takustr. 9, 14195 Berlin, the building itself is inset from the road and best accessed via a footpath from Arnimallee 6 (building with signature number Pi strip running along the walls)

The Institute is in the grey brick building on the ground floor, r. 005. See floor map

Nearest metro stop is U Dahlem-Dorf on the U3 line (walking distance 7 min. as seen on map)
Nearest bus stop is "Arnimallee" on the Bus X83 route (connecting U Dahlem with S+U Rathaus Steglitz).
The way to the workshop will be signposted from the top of Arnimallee.

Alternative access from the southside is via the Altensteinstraße 23 car park. Nearest busstop here is “Limonenstr." on the Bus 101 route. From car park follow the driveway until you arrive here. The workshop takes place in the grey brick building.

For official directions to institute and area map see here.
For googlemaps search use "Institute of Computer Science, 14195 Berlin"


Freie Universität does not operate on-campus guest houses or student dormitories. Therefore, participants from outside of Berlin must arrange their own accommodation. A good budget choice near campus is Residenz 2000 Aparthotel. For more links see the university's accommodation listing.
For a quick search of available accommodation use Set destination to "14195, Berlin" and "lowest price first". This should bring up numerous value deals within traveling distance from campus. The option “open in this map” is very useful in determining the distance from campus.Districts well connected to campus are Steglitz-Zehlendorf, Tempelhof-Schöneberg, Charlottenburg-Wilmersdorf as well as anything within the so called 'Ringbahn' loop. You can also check travel times from accommodation to FU on pubic transport journey planner

Getting around

Berlin has an extensive public transit network (undergound, urban rail, buses, trams) with 3 tariff zones. Ticket AB (2.80€) will get you anywhere in Berlin including Tegel Airport (TXL). For Schönefeld Airport (SFX) you will need Ticket ABC (3.40€). For more information see Tripadvisor Guide to Berlin Public Transport.


The workshop takes place during term break and the nearby student cafeteria will be closed. For lunch please bring your own provisions or use one of the following options:

FU Mensa | canteen | Otto-von-Simson-Str. 26 | menu | mensa card
Kantine Julius-Kühn-Institut | canteen |
Baci's Coffee | coffee shop | Königin-Luise-Str. 39 | soups, bagel, cakes
Asia Snack Dahlem | vietnamese | Königin-Luise-Str. 38
eßkultur in den Museen Dahlem | international | Takustr. 38-40 (via car park)


Name Mail
Katja Geiger general inquiries & registration katja.geiger[at]
Chris Wehmeyer coordinator christoph.wehmeyer[at]
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