Welcome to the hands-on section for the course of Computational Biophysics at the University of Trento for the a.y. 2019-2020.

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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 Thursday evening before the lecture.

List of tutorials and sources

  1. 2019.09.16 - Introduction & Visualisation with VMD
  2. 2019.09.22 - Fundamental ingredients of an MD simulation
  3. 2019.10.07 - Setting up a project + scripting your analyses
  4. 2019.10.14 - Setting a Namd simulation with thermostate and solvent
  5. 2019.10.21 - Namd@HPC, setting up Recoverin simulations
  6. 2019.10.28 - Recoverine wildtype, Recoverine mutations and git
  7. 2019.11.11 - Preliminary results + Membrane proteins 1.0
  8. 2019.11.18 - Membrane proteins 2.0
  9. 2019.11.25 - Membrane proteins 3.0 + mutated Recoverine in the membrane
  10. 2019.12.02 - Graphs, proteins, pyinteraph web servers for computational biophysics
  11. 2019.12.09 - Molecular Dynamics Flexible Fitting
  12. 2019.12.16 - Steered Molecular Dynamics

Conventions

Throughout the tutorial we will use the following colour code1.

Pay attention to this!

Useful(?) information.

Useful links.

Think about this question.

Bash shell commands/outputs

VMD tcl/tk console.

To improve readability, scripts will be formatted as:

#!/bin/bash

echo "This is a bash script."

Further readings

  1. The idea is taken from the colour scheme used by the Bonvin Lab for their course in Molecular Dynamics. ↩