@Sounak_Biswas, sure. Here is what the graph looked like of my peptide when I used xmgrace -nxy dssp_peptide_300_500ns.xvg to view the dssp plot in xmgrace.
Please note that if you don’t view the .xvg file with this command, it will not show the graph as you see it here. It will show differently otherwise, and it won’t include all of the aspects.
Just another thing I picked up: if you view this .xvg file in xmgrace with this command (xmgrace -nxy dssp_peptide_300_500ns.xvg), then it shows the secondary structure elements (loops, helices, turns, etc.) over the progression of your trajectory. It will not, however, show you which residues/regions of your protein adopt those specific secondary structures. So, if you’re just interested in how the secondary structure changes over your trajectory, it seems like the above command will do just that for you. But if you are more interested in which regions/residues your protein/peptide changed secondary structure during your trajectory, you might probably benefit more from the following links:
In this link, someone posted about a Python script they made that you can use to view the specific residues/regions of your protein and see the frequency of secondary structures those residues/regions adopted.
I hope it helps and all the best with this!
