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
--
========================================
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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