Welcome to the hands-on section for the course of Computational Biophysics at the University of Trento for the a.y. 2022-2023.

Lectures from the 2021-2022 course can be found here

Lectures from the 2020-2021 course can be found here

This website will collect all the tutorials presented during hands-on sessions. The material presented here will guide you in all practical steps needed to setup and run a simulation of a protein, and interpret its results.

Tutorials will be uploaded each Monday evening before the lecture (you will get an update on moodle).

List of tutorials and sources

  1. 2022.09.20 - Introduction & Visualisation with VMD.
  2. 2022.09.27 - Fundamental ingredient of an MD simulation.
  3. 2022.10.04 - Analyses of trajectories with VMD and MDAnalysis.
  4. 2022.10.18 - Running on HPC, benchmarks and restarts - Folder organization and GIT.
  5. 2022.10.19 - MDAnalysis: checking equilibration, block averaging
  6. 2022.10.25 - Protein-ligand complex preparation
  7. 2022.11.03 - Project presentation and membrane-protein set-up with CHARMM_GUI
  8. 2022.11.08 - Clustering and PCA
  9. 2022.11.15 - Graphs, proteins, and Pyinteraph - Webservers for computational biophysics - Reproducibility
  10. 2022.11.22 - Umbrella Sampling - set-up + simulation
  11. 2022.12.05 - CG simulations - ENM - Reproducibility - GIT

Additional tutorials

The tutorial below provides further material for the interested students.

  1. Beginners’ guide of the shell command line

Conventions

Throughout the tutorial we will use the following colour code1.

Pay attention to this!

Useful(?) information.

Think about this question.

Bash shell commands/outputs

Python or VMD tcl/tk console.

To improve readability, scripts will be formatted as:

#!/bin/bash

echo "This is a bash script."
  1. The idea is taken from the colour scheme used by the Bonvin Lab for their course in Molecular Dynamics.