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

RMSD moving residues