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270274 UE Computer laboratory: Computersimulation of Biopolymeres (2020S)

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


Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).


max. 10 participants
Language: German



Unless the situation changes for the better, the course will be held/taught remotely. More information to follow -- please make sure that mail sent to your unet account gets delivered.

Waehringerstr 17, 2nd floor, PC-Pool, 14:00-17:00

Tue 5.5, Thu 7.5
Tue 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)


Aims, contents and method of the course

From pdb file to CHARMM input; Manipulating structures and other aspects of the system with CHARMM. Computing energies, minimization. Introduction to molecular dynamics; analysis of trajectories -- comparison to experimental quantities; Overview of the "state of the art" (PME, NPT-simulations, GPU acceleration, ..); Setting up of a solvated systems; Final project (Setting up, carrying out and analysis of the simulation of a protein in water)

Assessment and permitted materials

Continuous evaluation of students' participation, completion of small exercises, protocol describing final project.

Minimum requirements and assessment criteria

1) Regular participation required (justified absences are OK, but need to be compensated by working remotely).

2) The individual units contain small controls/exercises intended to test the comprehension of the student. These are to be completed throughout the course and amount to a maximum of 12points.
3) Final project (setting up a simulation, simple analyses) (4 points) as well as a written protocol documenting the project (4 points).

Assuming sufficient presence/participation: > 18pts 'sehr gut'/very good, > 16 pts 'gut'/good, > 12pts 'befriedigend'/satisfactory, >=10pts 'genuegend' /acceptable.

Examination topics

Practical exercises using CHARMM

Reading list

see www.charmmtutorial.org

Association in the course directory

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

Last modified: Mo 30.03.2020 15:28