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
--
-------------------------
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 Thu Jul 26 2012 - 21:00:02 PDT
