[gmx-users] rmsd

Justin A. Lemkul jalemkul at vt.edu
Sun Mar 29 14:06:29 CEST 2009

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 


> 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


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