Analyzing Molecular Dynamics Data with PYTRAJ

This is the workshop material for a Molecular Dynamics course that is being developed and delivered by Compute Canada’s Molecular Modelling and Simulation Team.

Prerequisites

This material has been designed for a multi-day workshop offered by Compute Canada’s Molecular Modelling and Simulation Team and ACENET.

The procedure on how to setup, configure and start the Jupyter notebook server should work on all of Compute Canada’s clusters as well as all clusters using Compute Canada’s software stack. Data used in this material can be found here.

Schedule

Setup Download files required for the lesson
00:00 1. Using PYTRAJ in Jupyter Notebook What tools are available to analyze my MD-data?
How to setup Jupyter for simulation analysis?
00:25 2. Plotting Energy Components in Jupyter Notebook How to extract energy components from simulation logs?
How to load and plot energy components?
00:50 3. The Basics of PYTRAJ How to load MD-trajectories into PYTRAJ?
How to calculate RMSD to a reference?
01:15 4. Trajectory Visualization in Jupyter Notebook How to visualize simulation in Jupyter notebook?
01:40 5. Principal Component Analysis How to perform principal component analysis?
How to visualize principal components with VMD
02:05 6. Cross-correlation Analysis How to perform cross-correlation analysis?
How to visualize cross-correlation matrices
02:30 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.