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

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News

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:

General

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

Dates

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

Program

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

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

Wednesday 24: Free energies and rare-event kinetics

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

Friday 26: Presentations

All Presentations will be 15 minutes, plus short discussion.

Morning

Afternoon

Credit Requirements (Scheinkriterien)

Contact

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

Information for non-resident participants

Location

For directions and area map see here.

Accomodation

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.

Provisions

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.