Materials for the May 10, 2024 MDAnalysis workshop at University College London.
Richard Gowers - @richardjgowers
Micaela Matta - @micaela-matta
Harry Lewin (Teaching Assistant)
G15 Public Cluster, DMS Watson Building
University College London
Gower Street, London, WC1E 6BT
United Kingdom
See also accessibility information.
Garden Room, Wilkins Building
University College London
Gower Street, London, WC1E 6BT
United Kingdom
See also accessibility information.
| Time (BST) | Session | Materials |
|---|---|---|
| 9:00-9:15 | Check-In/Registration | |
| 9:15-9:25 | Opening Remarks and Introductions | |
| 9:25-10:45 | Session 1: MDAnalysis Basics and System Manipulation | Lecture 1, Tutorial 1 |
| 10:45-11:10 | ☕ break ☕ | |
| 11:10-12:30 | Session 2: Distances and Trajectories | Lecture 2, Tutorial 2 |
| 12:30-13:45 | Lunch | |
| 13:45-15:05 | Session 3: Analysis Tools | Tutorial 3 |
| 15:05-15:30 | ☕ break ☕ | |
| 15:30-16:50 | Session 4: Advanced Tips and Requests | Tutorial 4 |
| 16:50-17:00 | Closing Remarks |
Instructions for setting up your environment to run this workshop locally
are provided in INSTALL.md.
A full list of the required Python packages can be seen inside environment.yml.
As downloading and installing everything will take a little while, ideally you should follow these steps before the workshop starts. If you encounter any issues during installation, we can help!
Note: Materials may change between now and the time of the workshop, so while we ask you to install ahead of time, also make sure to git pull just prior to the start of the workshop.
If for any reason you cannot set up a local environment with all required packages, you can use Google Colab to run all workshop notebooks directly from your browser, no installation required.
| Session | Materials |
|---|---|
| Session 1: MDAnalysis Basics and System Manipulation |  |
| Session 2: Distances and Trajectories | |
| Session 3: Analysis Tools | |
| Session 4: Advanced Tips and Requests | |
The workshop assumes that attendees have a working knowledge of Jupyter notebooks, Python (especially the NumPy library), and the bash shell.
All members of the MDAnalysis community and participants in MDAnalysis workshops are expected to abide by the MDAnalysis Code of Conduct.
Written materials are provided under the CC-BY-4.0 SA license.
The MDAnalysis logo and its derivatives are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License.
Please see AUTHORS.md for a list of contributors to the workshop materials.
We would like to give a special thanks to our partners for this workshop, the Thomas Young Centre, the JCMaxwell Node of CECAM, and CCPBioSim.
This workshop has been made possible in part by a grant from the Chan Zuckerberg Initiative DAF, a donor advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989). MDAnalysis also thanks NumFOCUS for its continued support as our fiscal sponsor.
