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