[gmx-users] RMSF analysis

Justin Lemkul jalemkul at vt.edu
Wed Oct 9 21:47:30 CEST 2013

On 10/9/13 3:29 PM, Sainitin Donakonda wrote:
> Hi all,
> I recently performed MD simulation of protein - ligand complex..and
> analyzed its trajectory using RMSF tool in gromacs.
> This analysis revealed particular residue in binding site of protein showed
> quite high fluctuation around 0.30 nm but other residues were in range of
> 0.15 to 0.20
> Can any body explain why this particular residue have  high RMSF value in
> compared to other residues

Doubtful, at least not without considerably more information.  What functional 
significance does it have, if any?  What is the residue?  What did you measure - 
RMSF of the whole residue, just the backbone, just C-alpha, etc?

Higher RMSF means the residue flops around more, i.e. your outcome indicates 
that the residue deviates from the average position to a greater extent than the 
other residues.  Whether or not this actually means anything at all depends on 
your knowledge of the nature of the protein-ligand complex and the answers to 
the questions posed above.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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