RMSD fitting and analysis of a trajectory
Trajectory frames are going to be superimposed to a reference frame in
such a way that the root mean squared distance (RMSD)
\[\mathrm{RMSD} = \sqrt{\frac{1}{N} \sum_{i=1}^N (x_{a,i} - x_{b,i})^2}\]
is minimized.
Superposition
In order to more clearly show conformational changes, superimpose all
trajectory frames on the CORE domain using
- selection widget (starts with
protein
): enter the selection for
the CORE domain: protein and not (resid 30 to 59 122 to 159)
- Selection Modifiers: Backbone
- Reference Mol: Top
- RMSD: calculate RMSD (avg should be about 2.6 Å)
- ALIGN: superimpose all frames to the first frame
- RMSD: calculate RMSD (avg should be about 1.5 Å)
- to show CORE backbone RMSD over
time
- visualize the trajectory
RMSD analysis
Task: Produce a timeseries of the backbone RMSD of the whole protein
as a function of time (using )
Questions:
- What is the maximum RMSD?
- How does the RMSD change when you include
- all atoms?
- all heavy atoms (i.e., do not use hydrogens)?
- Does your RMSD result depend on the previous superposition step?
- Is the result consistent with the previous result of your RMSD
analysis of the static structures?