Event Downloads

Here, are all the instructions you will need for running the simulations and analysis of the workshop.

Colab Notebooks

The tool we will be using is Google Colaboratory. These notebooks connect you to a Google Machine running on a server that has access to 2 threads and, when required, to a high end GPU. Links will become available once the seminar has started.

SIRAH

This notebook was developed by Matías Machado and Pablo Galaz-Davison and provides the basics for running and analyzing data from the GROMACS MD engine running with the SIRAH forcefield.

Download

Fold-Switching

This notebook was developed by César A. Ramírez-Sarmiento and provides the basics for simulating and analyzing fold-switching dynamics through the GROMACS package.

Download

FrustratometeR

This notebook was developed by Maria Ines Freiberger and Pablo Galaz-Davison and provides the tools for basic usage of the FrustratometeR for analyzing energy frustration in proteins.

Download

Additional Tools

We recommend the download and installation of tools that may be extremely useful for the visualization of molecular dynamics or frustration.