301558 UE Exercises for Biomolecular Simulation (2020S)
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 06.02.2020 08:00 to Th 20.02.2020 18:00
- Deregistration possible until Th 20.02.2020 18:00
Details
max. 9 participants
Language: German
Lecturers
Classes
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, 14:00-17:00Tue 5.5, Thu 7.5Tue 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)
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 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%)
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
www.charmmtutorial.org
Andrew Leach "Molecular Modelling: Principles and Applications"
www.charmmtutorial.org
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