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270274 UE Computer laboratory: Computersimulation of Biopolymeres (2019S)
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 Fr 01.02.2019 08:00 to Su 31.03.2019 23:59
- Deregistration possible until Su 31.03.2019 23:59
Details
max. 10 participants
Language: German
Lecturers
Classes (iCal) - next class is marked with N
03.06.-19.06.2019
13-17h, Raeume des Instituts
- Monday 03.06. 13:00 - 17:00 Seminarraum 2 Währinger Straße 38 Dekanat 1. Stock
- Tuesday 04.06. 13:00 - 17:00 Carl Auer v. Welsbach-Hörsaal Chemie Boltzmanngasse 1 HP
- Wednesday 05.06. 15:00 - 18:00 Seminarraum 3 Organische Chemie 1OG Boltzmanngasse 1
- Thursday 06.06. 15:00 - 18:00 Seminarraum 3 Organische Chemie 1OG Boltzmanngasse 1
- Friday 07.06. 13:00 - 17:00 Seminarraum 3 Organische Chemie 1OG Boltzmanngasse 1
- Wednesday 12.06. 15:00 - 18:00 Seminarraum 3 Organische Chemie 1OG Boltzmanngasse 1
- Thursday 13.06. 14:00 - 18:00 Joseph-Loschmidt-Hörsaal Chemie EG Währinger Straße 42
- Friday 14.06. 13:00 - 17:00 Seminarraum 1 Analytische Chemie 2.OG Boltzmanngasse 1
- Monday 17.06. 13:00 - 17:00 Seminarraum 1 Analytische Chemie 2.OG Boltzmanngasse 1
- Tuesday 18.06. 13:00 - 17:00 Seminarraum 3 Organische Chemie 1OG Boltzmanngasse 1
- Wednesday 19.06. 13:00 - 17:00 Seminarraum 2 Währinger Straße 38 Dekanat 1. Stock
Information
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. Protocol describing final project
Minimum requirements and assessment criteria
1) Regular participation required (isolated absences are OK, but presence during 80% of the lab course required).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.
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
Last modified: Sa 08.07.2023 00:22