Universität Wien FIND

301558 UE Exercises for Biomolecular Simulation (2020S)

3.00 ECTS (3.00 SWS), SPL 30 - Biologie
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. 9 participants
Language: German



Unless the situation changes for the better, the course will be held/taught by e-learning. More information to follow -- please ensure that mail delivered to your unet address gets delivered.

Waehringerstr 17, 2nd floor, PC-Pool, 14:00-17:00

Tue 5.5, Thu 7.5
Tue 12.5, Thu 14.5
Tue 19.5, Wed 20.5
Tue 26.5, Thu 28.5
Wed 3.6, Thu 4.6
Tue 9.6, Wed 10.6
Tue 16.6, Thu 18.6 (only if needed)


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, final protocol.

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

Within the work environment, handouts and background material are provided
Andrew Leach "Molecular Modelling: Principles and Applications"

Association in the course directory

MMB W-3, MMB W-2

Last modified: Mo 30.03.2020 15:28