[gmx-users] Issue with RMSD profile

[Justin Lemkul]

On 4/26/13 9:33 AM, Sainitin Donakonda wrote:
> Hello all,
>
> I ran 10ns molecular dynamics simulation of protein ligand complex ..in
> which protein homology model..finally i analyzed .xtc file which is
> produced after MD production run..first i plotted RMSD profile of backbone
> of the protein ..it show that line starts from 0.2 nm to 0.4 nm and from it
> is stabilized in plateau..
>
> My question is  fluctuation in RMSD profile from 0.2nm to 0.4 nm is
> acceptable range or not?
>
> Can any body explain this
>

That sounds about reasonable for a normal, folded protein of average size, but 
do realize that a given value of RMSD basically tells you nothing.  More 
detailed assessment of the structure is required.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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