Materials for the October 25, 2023 MDAnalysis workshop.

Moderator: Jenna Swarthout Goddard

The workshop assumes that attendees have a working knowledge of MD 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 all 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!

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.