270040 PR Practical Course: Computersimulation of Biopolymeres (2024S)
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 Sa 03.02.2024 08:00 to Mo 26.02.2024 23:59
- Deregistration possible until Mo 26.02.2024 23:59
Details
max. 10 participants
Language: German
Lecturers
Classes
blocked from May to mid-June, independent work via Moodle/JupyterHub, regular office hours
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%)
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"
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, SHELL-Ergänzungsfach-Chemie, SHELL-Schwerpunkt-Chemie, CH-CBS-01, BC-CHE II-7
Last modified: Th 18.07.2024 14:06