Materials from this class were adapted from previous versions of the class and online workshops. Some of these sources may be useful to students of this class.

History

• In Spring 2020, I taught Chem 456 for the first time. Most of the examples were designed to be run in a computer lab.
• In Summer 2021, I organized An International Workshop in Modeling Biological Macromolecules and then ran a small session of Chem 456. Most examples were accessible through a virtual machine.
• In Spring 2022, I organized another version of the workshop, this time held in person in Baranquilla, Colombia. Lectures were simultaneously translated into Spanish! Examples were migrated to Google Colab, allowing easy access from computer with an internet connection.
• I also taught Chem 456 in Fall 2022 and Fall 2024. There have been some very successful student projects! This semester will be different because we will run Jupyter notebooks on ACCESS-CI resources instead of Google Colab. The interface is very similar, but ACCESS-CI has two key advantages: you will retain your virtual environment so that you don’t need to install packages before every exercise; and you can keep notebooks running for two days. It may require a bit more a learning curve in the beginning, but can ease a transition to batch jobs later in the class. Google Colab versions from Fall 2024 may be a useful backup if ACCESS-CI resources are not working.

Sources

In the Spring 2022 workshop, exercises were adapted from

• IIBM3202 Molecular Modeling and Simulation from the Institute for Biological and Engineering at Pontificia Universidad Catolica de Chile, and
• TeachOpenCADD