[gmx-users] RMSF analysis

[Gianluca Interlandi]

Is that residue in a loop?

Gianluca

On Wed, 9 Oct 2013, 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
>
> Thanks,
> Nitin
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-----------------------------------------------------
Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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