Welcome to the hands-on section for the course of Computational Biophysics at the University of Trento for the a.y. 2020-2021.

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 Tuesday evening before the lecture (you will get an update on moodle).

List of tutorials and sources

  1. 2020.09.21 - Introduction & Visualisation with VMD.
  2. 2020.09.23 - Python scripting & trajectory analysis.
  3. 2020.09.30 - Fundamental ingredients of an MD simulation.
  4. 2020.10.07 - Simulating membrane proteins 1. charmm-gui.
  5. 2020.10.14 - Research project presentation - protein ligand complex preparation
  6. 2020.10.28 - MD@HPC - Reproducible computational science 1. - Trajectory analysis
  7. 2020.11.04 - SBDS in more details, introducing mutations, preparing the system.
  8. 2020.11.11 - Clustering and PCA
  9. 2020.11.18 - Reproducible computational science 2:Git - Graphs, proteins, pyinteraph
  10. 2020.11.25 - Advanced topics: Umbrella sampling
  11. 2020.12.02 - Advanced topics: Brownian-dynamics simulations of nucleic-acids with lammps.
  12. 2020.12.09 - Advanced topics: TBA.

Additional tutorials

The tutorials below provide further material for the interested students.

  1. More advanced VMD and TCL scripting
  2. 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.