Hi,
On Fri, Apr 10, 2015 at 4:44 PM, Jose Borreguero <borreguero.gmail.com> wrote:
> Is it the fluctuations of the center of mass of the first residue, or the
> average of the atomic fluctuations for the atoms in the first residue? I
> could not get a clear cut answer from the manual.
Sadly this is sometimes the case, although I promise you we are
constantly working to make the manual better!
Here your second guess is correct; when 'byres' is specified the
mass-weighted atomic fluctuations of each atom in the residue are
averaged like so:
ResidueFluct = SUM[ AtomFluctX * massX ] / TotalMass
'bymask' is similar except the averaging occurs over the entire atom mask.
Hope this helps, and thanks for pointing out the omission in the manual.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Apr 13 2015 - 09:00:03 PDT
