[gmx-users] Output for rmsd and radius of gyration doubts

Justin Lemkul jalemkul at vt.edu
Tue Feb 26 03:54:30 CET 2013

On 2/25/13 9:38 PM, Ewaru wrote:
> Hi,
> Just need some advice regarding the following results I obtained while
> following the tutorial from this site, using a protein structure that I
> modelled using Modeller.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
> 1. My output plot of RMSD doesn't converge. (From 0 - 0.4ns, its around
> 0.25nm, 0.4 - 0.7, around 0.3nm, 0.7 - 1.0ns, around 0.35). Does it mean
> that my EM wasn't properly done? Anyway, the EM did not reach the requested
> Fmax <100.
> 2. My graph for Radius of gyration from 800 - 1000ps shows a higher
> fluctuation than the ones from 0 - 800ps. Does it mean that the structure is
> not that stable?
> Please advice. (I followed exactly the steps in that tutorial. I'm new to
> Gromacs.) And of course, I neutralized my protein according to the charge
> needed. Not exactly following blindly from the tutorial. ;)

Please don't assume that 1 ns of MD for any system is actually meaningful, or 
that the results of some other protein will necessarily look anything like my 
example.  The commands in the tutorial are just to show how one might go about 
doing analysis and demonstrating a few tools that can be used.  Most protein 
systems require tens, if not hundreds, of ns to manifest the behavior of 
interest.  The results you've posted indicate nothing more than the fact that 
your protein isn't yet anywhere close to equilibrium, which is not at all 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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