From: Vermaas, Josh (
Date: Mon May 30 2022 - 15:52:12 CDT

Do you end up doing alignment in this process? RMSF is calculating the deviation relative to an average structure, and that average structure depends on how the alignment is done. In the first round, you were likely aligning to both proteins simultaneously. In the second, each protein is aligned independently. Id expect the answers to be subtly different, but broadly comparable.


From: <> on behalf of Efthymiou, Christos <>
Date: Monday, May 30, 2022 at 3:57 PM
To: <>
Subject: vmd-l: Clarification on RMSF Calculation

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?