From: Efthymiou, Christos (
Date: Mon May 30 2022 - 14:08:16 CDT


I have run a simulation on a protein-protein complex and I am using the QwikMD extension to run some analysis on the simulation.

When I calculate the RMSF vs Residue Number using the default selection of protein, I get RMSF values up to residue 352. I have two proteins in the simulation, one of which is numbered 1-294 and another 1109-1166. Based on this, I would assume residues 295-352 correspond to 1109-1166.

However, if I then calculate the RMSF with the selection of chain A (1-294) and chain C (1109-1166) separately, the numbers do not match the RMSF calculation for the protein selection. For example, on the left I have the RMSF calculation when protein was used as the selection and on the right is when chain A was used as the selection.


I have also compared the RMSF calculation with selection of chain C compared to residues 295-352 from the protein selection, and those numbers also do not match.

Therefore, which selection is correct? And why do the numbers not match?