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301577 VO Biomolecular Simulation Techniques (2021S)

REMOTE

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

Digital
March through May, every Wednesday 14:15-15:45

Wednesday 03.03. 14:15 - 15:45 Digital
Wednesday 10.03. 14:15 - 15:45 Digital
Wednesday 17.03. 14:15 - 15:45 Digital
Wednesday 24.03. 14:15 - 15:45 Digital
Wednesday 14.04. 14:15 - 15:45 Digital
Wednesday 21.04. 14:15 - 15:45 Digital
Wednesday 28.04. 14:15 - 15:45 Digital
Wednesday 05.05. 14:15 - 15:45 Digital
Wednesday 12.05. 14:15 - 15:45 Digital
Wednesday 19.05. 14:15 - 15:45 Digital
Wednesday 26.05. 14:15 - 15:45 Digital

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)

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://scc.acad.bg/ncsa/articles/library/Library2016_Supercomputers-at-Work/Molecular_Dynamics/Elements-of-Molecular-Dynamics-Smith%20.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

Last modified: We 24.01.2024 00:24