Universität Wien

270274 UE Computer laboratory: Computersimulation of Biopolymeres (2022S)

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

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).

Details

max. 15 participants
Language: German

Lecturers

Classes (iCal) - next class is marked with N

Tentatively scheduled from May 9 to June 11, 2022
While there are formally no prerequisites, it is recommended to follow the lecture course with the saem title (unless you have relevant prior knowledge!)

The lab course is hosted via Moodle and a J(upyter)H(ub) Server hosted by central IT services. Introductory meetings either in person or via Zoom; they will be recorded.

You are free to choose you schedule, but there is a lot of material so you should work regularly on the JH Server

  • Wednesday 11.05. 12:00 - 12:45 Kleiner Hörsaal 3 Chemie Boltzmanngasse 1 HP
  • Wednesday 18.05. 12:00 - 12:45 Kleiner Hörsaal 3 Chemie Boltzmanngasse 1 HP
  • Wednesday 25.05. 12:00 - 12:45 Kleiner Hörsaal 3 Chemie Boltzmanngasse 1 HP
  • Wednesday 01.06. 12:00 - 12:45 Kleiner Hörsaal 3 Chemie Boltzmanngasse 1 HP

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 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 protocols (30%)

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"

Association in the course directory

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

Last modified: Sa 08.07.2023 00:22