Materials for the February 28, 2024 MDAnalysis and Molecular Nodes workshop. The recording of this workshop is available on the MDAnalysis YouTube channel.
Each section will consist of a lecture component, introducing relevant concepts, and a guided tutorial component which you can follow along with the instructor (or at your own pace).
Moderators: Lily Wang and Brady Johnston
| Time | Topic | Instructor |
|---|---|---|
| 03:00 - 03:05 UTC | Introduction | |
| 03:05 - 04:15 UTC | MDAnalysis Part 1 (basics, system manipulation) Lecture ,1 / Tutorial 1 | Fiona Naughton |
| 04:15 - 04:20 UTC | Q&A / Break | |
| 04:20 - 05:30 UTC | MDAnalysis Part 2 (distances, trajectories) Lecture 2 / Tutorial 2 | Lily Wang |
| 05:30 - 05:35 UTC | Q&A / Break | |
| 05:35 - 06:45 UTC | Molecular Nodes Tutorial / Blender Notebook Tutorial | Brady Johnston, Yuxuan Zhuang |
| 06:45 - 06:50 UTC | Final Announcements | |
| 06:50 - 07:00 UTC | Final Q&A |
The workshop assumes that attendees have a working knowledge of MD (molecular dynamics) simulation workflows, Jupyter notebooks, Python (especially the NumPy library), and the bash shell.
If for any reason you cannot set up a local environment with all required packages as explained below, you can use Google Colab to run the MDAnalysis workshop notebooks directly from your browser, no installation required.
| Session | Materials |
|---|---|
| Lecture 1: MDAnalysis Basics |  |
| Tutorial 1: System Manipulation and Atom Selection | |
| Lecture 2: Distance Calculations | |
| Tutorial 2: Distances and Trajectories | |
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.
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.
This workshop has been made possible in part by a grant from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989). MDAnalysis also thanks NumFOCUS for its continued support as our fiscal sponsor.