Welcome to the hands-on section for the course of Computational Biophysics at the University of Trento for the a.y. 2021-2022.

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. 2021.09.21 - Introduction & Visualisation with VMD.
  2. 2021.09.28 - Analyses with VMD and MDAnalysis.
  3. 2021.10.05 - Fundamental ingredient of an MD simulation.
  4. 2021.10.12 - Running on HPC, benchmarks, restarts, quick python recap.
  5. 2021.10.19 - Python, checking equilibration, block averaging
  6. 2021.10.26 - Protein-ligand complex preparation
  7. 2021.11.02 - Project presentation and membrane-protein set-up with CHARMM_GUI
  8. 2021.11.09 - Clustering and PCA
  9. 2021.11.16 - Graphs, proteins, and Pyinteraph - Webservers for computational biophysics
  10. 2021.11.23 - Reproducible Science & git
  11. 2021.11.30 - Umbrella Sampling - setting up + simulation
  12. 2021.12.07 - Overview of CG simulations of large systems + Projects discussion.

Additional tutorials

The tutorial below provides further material for the interested students.

  1. Installing Pyinteraph for Python 2.7 with Conda


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:


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.