From: John Stone (
Date: Tue Jan 07 2020 - 14:34:51 CST

RMSF is a measure of fluctuation over potentially many frames (not just
between a pair), RMSD is a measure of deviation between a pair of frames.
Much more could be said, but the RMSF per residue calculation in VMD
computes centers of mass for each residue for all frames and computes
the variance vs. the original reference frame.

  John Stone

On Thu, Dec 19, 2019 at 12:04:19AM +0530, Ashraya Ravikumar wrote:
> Hi All,
> What is the conceptual difference, if any, between calculating
> RMSD-per-residue and calculating residue-wise RMSF in a trajectory?
> Regards,
> Ashraya

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