Hi,
Without knowing how the RMSD and RMSF was calculated (i.e. what
commands were used) it's difficult to answer your question precisely.
RMSD and RMSF are inherently different measures; RMSD is a measure
reflecting deviation of all coordinates from reference coordinates for
each frame, while RMSF reflects the overall movement of atoms (or
residues depend on your output type) over all frames. So large overall
fluctuations in one part of the protein may or may not be reflected in
your RMSD values depending on how the rest of your system is moving,
what reference structure you're using for the RMS calc, etc.
Note that the 'atomicfluct' command does not implicitly perform any
fitting of coordinates, so if you don't RMS-fit your structures to
something like an average reference structure your fluctuations will
reflect global translational/rotational motions as well. From the
'atomicfluct' entry in the AmberTools 13 manual:
"If you want fluctuations without rotations or translations (for
example to the average structure), perform an RMS fit to the average
structure (best) or the first structure (see rmsd) prior to this
calculation."
Hope this helps,
-Dan
On Fri, Jun 14, 2013 at 9:57 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi,
>
> Recently, one of my lab mates ran an MD simulation and she generated both RMSD and RMSF graphs (nobox). We then observed that while the RMSD value is ~ 3 Angstroms, the RMSF reached as high as 10 Angstroms and as low as 5 Angstroms. Therefore, I'm wondering if it's possible to have RMSF values larger than RMSD values, because logically if a large RMSF is observed, it should be captured in RMSD since it's calculated over time. What do you guys think?
>
> Regards
> Yip Yew Mun
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jun 14 2013 - 10:00:02 PDT
