2024-MolSim-UniPD

Material for the Molecular Simulations module (for Prof. Fuxreiter)

Toni Giorgino

How to run

The code contained in this repo is structure in large part as IPython notebooks. They can be run in three ways:

• On your local machine. That's probably the easiest and most didactic for interpreting the intermediate files.
• On Google Colab. Just open Colab and point it to the file's URL. Simulations run much faster if you request a GPU runtime.
• On Binder. Somewhat slow but comes with a pre-installed environment. Open in binder

Day 2

Here are the links:

• Analysis with MDTraj: https://github.com/giorginolab/MD-Tutorial-Data/blob/main/notebooks/2_MDTraj_analysis.ipynb . If "open in Colab" does not work automatically, manually open Colab and point it to said address.
• Docking: https://github.com/giorginolab/2024-MolSim-UniPD/blob/main/docking/Docking_2024.ipynb or here . Same as above.

Remember that we use condacolab, so there will be an initial restart of the kernel.