Re: [AMBER] RMSD vs RMSF vs nofit-RMSD

From: Daniel Roe <>
Date: Fri, 27 Dec 2013 07:01:12 -0700


On Thu, Dec 26, 2013 at 10:40 AM, Nitin Sharma <>wrote:

> I know the definition of RMSD, RMSF and nofit-RMSD i.e. RMSD calculates
> the RMSD by fitting over the reference structure provided by the user. RMSF
> calculates RMSD but with respect to the average structure and nofit-RMSD
> calculates RMSD without fitting against the provided reference. Therefore
> the they give different results.

RMSF is a fundamentally different calculation than RMSD. RMSF (the
'atomicfluct' command in cpptraj/ptraj) is a local measure of motion; it
measures the mean fluctuation of atoms, i.e. how much each individual atom
moves around (the 'byres' keyword simply averages the results for each atom
on a per-residue basis). It is recommended that you RMS-fit to an averaged
structure prior to using the 'atomicfluct' command in order to remove
global rotational/translational motion, but the fitting is not part of the
RMSF calculation itself.

What I should use when I want to see the influence of the mobility of
> particular residues on ligand binding interaction?

For this I think that you can use either 'rmsd' with the 'perres' keyword
to calculate per-residue RMSD (which is a global RMS-fit followed by a
no-fit RMSD calculation for individual residues), or 'atomicfluct' with the
'byres' keyword.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Dec 27 2013 - 06:30:02 PST
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