301577 VO Biomolecular Simulation Techniques (2023S)

Moodle

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).

Details

Language: German

Examination dates

Lecturers

Classes (iCal) - next class is marked with N

The lecture will take place from March 1, 2023 till June 7, 2023 every Wednesday from 13:15-14:45 in HS 4 Chemie (Waehringerstr 42, 1090).

Tentative exam dates (digital via Moodle, 18:30-19:45): June 15, July 13, September 15, mid-February 2024

Wednesday 01.03. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 08.03. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 15.03. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 22.03. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 29.03. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 19.04. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 26.04. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 03.05. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 10.05. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 17.05. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 24.05. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42
Wednesday 31.05. 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42

Information

Aims, contents and method of the course

Introduction in molecular dynamics (MD) simulations of biopolymers

1) Some physics background (class. mechanics, stat. thermodynamics)

2) Important methods and algorithms, such as the Verlet family of integrators, force field terms, efficient calculation of nonbonded interactions, SHAKE, thermostats, barostats, particle-mesh Ewald method etc.
3) Methods building upon MD, e.g., calculation of free energy differnces
4) Practical setup of simulations, from PDB file to simulation system

Assessment and permitted materials

Digital written exam with questions for download (open book, but a fixed time window)

Four dates will be offered, tentively
June 15, 2022
July 11, 2022
Sep 15, 2022
and mid-December 2022

Minimum requirements and assessment criteria

50% of the possible exam points

Examination topics

See aims and topic of course

The exam questions will probe your knowledge of the methods used in MD simulations. The will also be concerned with the setup of meaningful simulations systems which represent reality as much as possible.

Reading list

Additional background reading:

1) Background on methodology

https://www.ccp5.ac.uk/sites/www.ccp5.ac.uk/files/DL_POLY/data/4.09/EoMD.v1.2.pdf

(To the best of my knowledge the above PDF is in the public domain; I can make a local copy available)

2) Setting up meaningful simulation systems:
http://charmm-gui.org/?doc=demo

Association in the course directory

MMB W-3, MMB W-2, MMB II.

Last modified: Tu 10.10.2023 12:28