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

From: vadiraj kurdekar <>
Date: Fri, 27 Dec 2013 18:34:33 +0800 (SGT)

in MD if you want to monitor mobility of any residue over a time period then rmsf is useful. and if just want to compare before and after binding them RMSD or nonfit- RMSD (for whole protein or only residue that you are monitoring) is useful.
With Regards,
Vadiraj Kurdekar,
Research Scholar, Pharmacy Dept.,
Birla Institute of Technology and Science-Pilani,
Pilani Campus, 
Rajasthan, PIN: 333031


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On Thursday, 26 December 2013 11:13 PM, Nitin Sharma <> wrote:
Respected sir,

This might be very silly but I hope you can help me to clarify few things.

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.

Now my question is what to use in which scenario? What is difference in application of the RMSD, nofit-RMSD and RMSF ?

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

Thanks in advance.

Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore :<> ; linkedin<>

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Received on Fri Dec 27 2013 - 03:00:02 PST
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