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 Graphics ‣ Representations in the 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.