RMSD values are typically calculated for a specific selection (e.g. in VMD, MDAnalysis, ...). So it is easily possible to calculate individual RMSD values for proportions of your molecular system. The problem is, that RMSD calculations highly depend on alignment. If you would like to calculate the displacement in a protein environment, you should align the system on the protein but if you are interested in the conformational fluctuations of the peptide, the alignment should be performed with the peptide only.

Thank you for the answer, Dr Lukas Schulig

If you want more control over this I can recommend writing your own script for the RMSD calculations using a package like biotite in python.

(Here is an example on how to analye an MD including RMSD calculation with explicit alignment:

https://www.biotite-python.org/examples/gallery/structure/md_analysis.html#sphx-glr-examples-gallery-structure-md-analysis-py).

Thank you, Benjamin E. Mayer . It seems interesting.