This tutorial shows how to analyze molecular dynamics trajectories, including essential dynamics analysis. This tutorial shows frame-by-frame analysis of trajectories, so it is particularly helpful for analysis of long trajectories that do not fit in your computers memory.

Required Programs

Latest versions of ProDy and Matplotlib are required.

Getting Started

To follow this tutorial, you will need the following files:

 8.4M Apr 27 11:03 mdm2.dcd
 112K Apr 27 11:03 mdm2.pdb
 8.4M Apr 27 11:03 mdm2sim2.dcd

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

or with pylab environment:

$ ipython --pylab

First, we will make necessary imports from ProDy and Matplotlib packages.

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

We have included these imports in every part of the tutorial, so that code copied from the online pages is complete. You do not need to repeat imports in the same Python session.