Molecular Dynamics tutorial

Status Documentation Status
Last modified Apr 20, 2017

Molecular dynamics tutorial presenting posibilities given by vanila python and open source Python libraries.

Tutorial covers in details creating and analyzing trajectories produced by the most popular simulation packages. It also contains several good practices borrowed from software engineering like: version cotrol, workflow automation, data piplines, and scaling up / scaling out computation.

What you will learn

  • what are most popular tools to do MD
  • popular data formats and python tools to work with them
  • how to prepare robust and easy to set up work environment
  • how to build MD system
  • how to run MD simulations using most popuar packages
  • how to dock small ligands
  • how to scale up/out your simulations
  • how to load a structure or a MD trajectory (popular formats)
  • how to select parts of your system
  • how to work with atoms, residues and molecules
  • how to deal with large data-sets (bigger than RAM)
  • how to analyze MD trajectories
  • how to write out or convert trajectories
  • how to use various algorithms in analysis (clusterization, structure, ML)
  • how to build interactive visualizations

Indices and tables