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301577 VO Biomolecular Simulation Techniques (2024S)

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

I want the set exam dates (held digitally) in accord with your wishes. My plan (plus/minus a few days):

Juni 19, 2024
Juli 15, 2024
September 17, 2024
Mid-December 2024 or Mid-January(2025)

Lectures:
Mittwoch 06.03.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 13.03.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 20.03.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 10.04.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 17.04.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 24.04.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 08.05.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 15.05.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 22.05.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 29.05.2024 13:15 - 14:45 Hörsaal 4 Chemie HP Währinger Straße 42 2H23
Mittwoch 05.06.2024 13:15 - 14:45 Seminarraum 2 Währinger Straße 38 Dekanat 1. Stock 2124

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 II., MMB IV.

Last modified: Th 07.11.2024 10:46