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

[Justin Lemkul]

On 3/4/13 9:49 AM, Ewaru wrote:
> Hi Justin,
>
> I tried running the simulation for 10ns and this time, my RMSD graph shows a
> stable fluctuation of 0.45nm from 2.5ns to 10ns. The radius of gyration
> shows stable fluctuation from 4ns to 10ns around 2.46nm. My doubt is,
> shouldn't the RMSD be fluctuating at 0.1nm? Does it mean that my structure
> is not stable? Or do I need to run more than 10ns of simulation?
>

Why would you assume that your RMSD would be 0.1 nm?  That's quite low, even for 
the most stable of proteins.

> Please advice. :(
>
> I attached a screenshot of the graph in case I didn't explain it well.
>
> g_rms
> http://postimage.org/image/f4bkobtx9/
>
> g_gyrate
> http://postimage.org/image/gd86i2jpj/
>

Protein properties fluctuate over time, and can correspond to behaviors that are 
both subtle and obvious.  Small changes in secondary structure can account for 
fluctuations in RMSD, larger domain motions or loop regions flopping around 
would explain larger spikes in RMSD or Rg.

I don't know what system you're working with or what your goals are, but in 
general, 10 ns is still considered very short for all but the fastest motions in 
proteins.  Domain motions and other tertiary movements may take anywhere from 
tens or hundreds of nanoseconds to the microsecond time frame.

-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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