shahrbanoo karbalaee wrote:
Dear justin
I have rmsd graph from peptide (13 amino acid).would you please tell
me about generally range of rmsd for good simulation.In my table rmsd
start from 2 nm and come up to 3 and change between 3 to 3.5
nm.the solvent is tfe/water.thanks for your advise.
I would argue that there is no such thing as a generalized "good" RMSD. It is
entirely dependent upon the stability of your protein, the solvent conditions,
and whether or not you have appropriate simulation parameters. Check for
stability in the RMSD value over time, and whether or not the behavior you are
seeing in the simulation makes sense based on what is known experimentally (if
possible).
-Justin
best regards
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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