Hi Dan,
First of all thanks for your prompt response !
So as I supposed (was not sure) without the "mass" keyword radgyr behaves
in the same
way like the older version. I was just confused with the "max radius of
gyration"
naming, which is not so lucky one in my opinion.
Regarding to "center of geometry" (COG) versus "center of mass" (COM)
here, if I understood well
COM is used only if "mass" keyword is used which unfortunately also means
that
the Rg is mass-weighted in other word there is no possibility in actual
version
to calculate Rg as it is defined (with respect to COM but without
mass-weights) am I right ?
Fortunately for many molecules (thanks to their "mass homogeneity")
COG and COM are probably not so different and this difference is perhaps
within
the tolerance of relevant experimental methods (small-angle scattering
techniques)
which results are often compared to that computational.
Just last detail:
You wrote that : "The distance of each atom from the center is weighted by
its mass"
but considering the formula you provided:
RoG = Sqrt( SUM[ (Ri - Rc)^2 * Mi ] / Mtotal)
I would rather say that the SQUARE of the distance of each atom from the
center is mass weighted or relative mass wighted as I may also introduce
relative mass Mi_r = Mi/Mtotal here
and write your formula this way:
RoG = Sqrt( SUM[ (Ri - Rc)^2 * Mi_r ] )
But anyway for me would be very interesting to know what was the
inspiration to introduce
this new Rg variant which has indeed more information inside than the
common Rg
(without mass weighting) so it may clearly distinguish molecules with the
very similar
shape and size but differing in chemical composition.
Is there for example any experimental technique which can estimate this
quantity ? or it was introduced from other reasons ( fitting purposes
etc. ) ?
Best wishes,
Marek
Dne Fri, 27 Jul 2012 05:45:06 +0200 Daniel Roe <daniel.r.roe.gmail.com>
napsal/-a:
> Hi,
>
> On Thu, Jul 26, 2012 at 10:30 AM, Marek Maly <marek.maly.ujep.cz> wrote:
>> #1
>> How is then defined "max radius of gyration" of the given set of atoms ?
>> a)
>> Rg is calculated/defined with respect to the center of mass (COM)
>> automatically or the default option in Amber is to use just geometric
>> center instead COM ?
>
> It is the maximum distance (i.e. the largest [Ri - Rc]) observed
> during the summation over all atoms in the mask, where Ri is position
> of atom i and Rc is position of the center of all atoms in mask
> (either geometric center or center of mass depending on the mass
> keyword).
>
>> #2
>> What does it mean exactly the sentence:
>>
>> "If the mass keyword is specified the radius of gyration will be
>> calculated with respect to the center of mass of atoms in <mask>, and
>> will
>> be massweighted."
>
> The distance of each atom from the center is weighted by its mass.
>
> RoG = Sqrt( SUM[ (Ri - Rc)^2 * Mi ] / Mtotal )
>
> where Mi is the mass of atom i and Mtotal is the sum mass of all atoms
> in the mask. When not mass weighted Mi is always 1.0 and Mtotal is
> just the number of atoms in the mask (N). Note that also when
> mass-weighted the max atom distance is also weighted by its mass.
>
> Hope this helped,
>
> -Dan
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 27 2012 - 06:00:04 PDT
