301558 UE Exercises for Biomolecular Simulation (2023S)
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 09.02.2023 08:00 to Th 23.02.2023 18:00
- Deregistration possible until Th 23.02.2023 18:00
Details
max. 10 participants
Language: German
Lecturers
Classes
Tentatively scheduled from April 17 to May 31, 2023, with latest hand-in of exercises by June 15. Moodle is now accessible. During the duration of the course I'll offer office hours once a week to discuss/work on problems/issues which cannot be resolved remotely (e-mail, etc.). Details to follow once I have a room
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 Google Meet; 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 ServerInformation
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 protocol (30%)
Prompt completion of questions / small exercises testing the course content (40%)
Final project, short protocol (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"
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 W-3, MMB W-2, MMB II, MMB III 4a.
Last modified: Tu 18.04.2023 09:50