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270274 UE Computer laboratory: Computersimulation of Biopolymeres (2021S)

3.00 ECTS (3.00 SWS), SPL 27 - Chemie
Continuous assessment of course work


Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).


max. 15 participants
Language: German



-digitale Lehre-

The course will be held remotely during a period of 6 weeks, starting mid/end of May. There are no fixed course times, so you can work through the course material at your own pace. The raw working time is approximately 10-12 half-days.

Question/Answer sessions and time slots on high end graphics machines in our lab will be scheduled (on demand and circumstances permitting) during the actual course

The primary workt tool is your laptop / computer!

More information to follow on Moodle and related platforms which will be used


Aims, contents and method of the course

The course is a comprehensive introduction into setting up and carrying up molecular dynamics simulations of biomolecular macromolecules. Topics covered include: force field terms, minimization, numerical integration of equations of motion, thermostats, barostats, periodic boundary conditions and Ewald summation. Basic analysis techniques are illustrated.

Students work in a locally hosted web-based Linux environment, in which most relevant programs (in particular CHARMM) are available. Work can be continued from home, using one's personal computer/laptop. Visualization is carried out using VMD, installed on the machines of the PC Pool, and freely available for Linux, Windows and Mac. In the final phase of the course, heavy use is made of www.charmm-gui.org to set up simulations.

Assessment and permitted materials

Continuous evaluation of students' participation, completion of small exercises, protocol describing final project.

Minimum requirements and assessment criteria

The factors contributing to the grade listed below in the field "Pruefungstoff" lead to a maximum of 6+8+6=20 points. For a passing grade ("genuegend" (4)) 10 points are needed.

Examination topics

Regular participation (30%)
Prompt completion of questions / small exercises testing the course content (40%)
Final project, short protocol (30%)

Reading list

see www.charmmtutorial.org
Andrew Leach "Molecular Modelling: Principles and Applications"

Association in the course directory

CHE II-7, MMB W-3, SHELL-Ergänzungsfach-Chemie, SHELL-Schwerpunkt-Chemie, TC-3

Last modified: Mo 01.03.2021 08:48