This was addressed recently on the list, check the archive. It depends on
the mask and the fitting for each case (rmsd and rmsf). I suspect in your
case they are not the same.
On Jun 14, 2013 11:59 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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Received on Fri Jun 14 2013 - 09:30:02 PDT
