Team:EPF-Lausanne/Analysis

Equilibrium

RMSD for individual residues

We aim at finding the average RMSD over time for each residue in the protein using VMD.

1. We load the .psf and .dcd files obtained after the first round of simulation.

2. In the TkCon window type:

source residue_rmsd.tcl

set sel_resid [[atomselect top "protein and ] get resid]

This will get all the residues number of all alpha-carbons in the protein. Since there is just one and only one α-carbon per residue, it is a good option.

3. Now we will calculate the RMSD values of all atoms in the newly created selection:

rmsd residue over time top $sel resid

At the end of the calculation, we have a list of the avergae RMSD per residue (in the file residue_rmsd.dat)

4. In VMD, in Graphics → Representations, do the following actions:

• create two replicates: protein and resname FMN in selected atoms
• for the FMN, choose CPK as a drawing method
• for the protein, choose tube as drawing method, and user as coloring method. Now click on the Trajectory tab, and in the Color Scale Data Range, type 0.40 and 1.00.

The protein is colored according to its average RMSD values. The residues displayed in blue are more mobile while the ones in red move less.

Here is a movie with the protein colored according to average RMSD values.

RMSD moving residues

5. Now we can plot the RMSD value per residue by typing in a Terminal window :

xmgrace residue rmsd.dat

We obtain the following picture: