.. -*- coding: utf-8 -*-

=======================
 MD analysis exercises
=======================

Analyze the **topology file** *1ake_nowater.psf* with the **trajectory
file** *1ake_nowater.xtc*.

- Visualize the trajectory (superimpose on the CORE domain) and
  describe the behavior.  (Note: the trajectory can be smoothed by
  setting a :guilable:`Trajectory Smoothing Window Size` of *2* under
  :menuselection:`Graphics --> Representations` in the
  :guilabel:`Trajectory` tab for the protein atoms.)
- Produce a RMSD timeseries (for the backbone of the full protein).
- Use a distance measure to quantify the observed conformational
  changes.