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301558 UE Exercises for Biomolecular Simulation (2026S)
Continuous assessment of course work
Labels
Registration/Deregistration
Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).
- Registration is open from Th 12.02.2026 14:00 to Th 26.02.2026 18:00
- Deregistration possible until Th 26.02.2026 18:00
Details
max. 20 participants
Language: German
Lecturers
Classes
The course will be held in blocked form approximately between the beginning of May and mid-June. The work will be done via the University of Vienna's Moodle/JupyterHub server. You are free to organize your time as you wish, but the protocols must be submitted (via Moodle) on time. I will provide more detailed information later.
Information
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 web-based Linux environment (JH Server, hosted by central IT), 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 and protocols, to be uploaded via Moodle.
Minimum requirements and assessment criteria
The factors contributing to the grade listed below in the field "Pruefungstoff" lead to a maximum 20 points. For a passing grade ("genuegend" (4)) 10 points are needed.
Examination topics
Regular participation; despite free organization of time try to stay on top of the exercises/workbooks (40%)
Prompt completion of questions / small exercises testing the course content (60%)
Prompt completion of questions / small exercises testing the course content (60%)
Reading list
see 1) www.charmmtutorial.org
2) At www.charmm-gui.org you can find tutorials i) for Unix, Python, PDB Files und CHARMM, as well as various video tutorials ii) which illustrate the preparation / set up of systems before starting an MD simulation.
Andrew Leach "Molecular Modelling: Principles and Applications"
2) At www.charmm-gui.org you can find tutorials i) for Unix, Python, PDB Files und CHARMM, as well as various video tutorials ii) which illustrate the preparation / set up of systems before starting an MD simulation.
Andrew Leach "Molecular Modelling: Principles and Applications"
Association in the course directory
MMB III 1a:, MMB IV.
Last modified: Fr 30.01.2026 07:07