Practical sessions

This page contains files for the practical sessions of the ASU course Simulation Approaches to Bio- and Nanophysics. Unless otherwise specified, material is provided under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 license.

  1. Session 01: Introduction to Unix and the Bash shell; see also Introduction to Unix
  2. Session 02: Bash shell scripting; for using the vi editor see vi essentials
  3. Session 03: Python
  4. Session 04: Python and NumPy arrays
  5. Session 05: Practical excercises
  6. Session 06: Plotting and the Verlet integrator
  7. Session 07: Verlet integrator in 3D: bond dynamics and trajectory visualisation
  8. Session 08: Design of the midterm project
  9. Session 09: Protein structure and visualization
  10. Session 10: Protein dynamics and visualization
  11. Session 11: LJ fluid in Gromacs
  12. Session 12: Using saguaro
  13. Session 13: Simulation of AdK in water
  14. Session 14: Thermostat
  15. Session 15: MDAnalysis

Midterm project

The Midterm project directory contains material for the midterm project (Feb 21, 2013 -- Mar 13, 2013).

See also the Midterm Wiki on Blackboard, under Tools/Wikis:Miderm project 2013.

Final project

See the documents on Blackboard.

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License