Hi all,
I have just some questions regarding actual "radgyr" command.
In AmberTools12 manual is actually written this description:
-------------------------------------------------------------------------------------------------
radgyr [<dataset name>] [<mask>] [out <filename>] [mass] [nomax]
Calculate the radius of gyration of atoms in <mask> (all atoms if no mask
specified). Output
radius of gyration and max radius of gyration to <filename>. If the nomax
keyword is specified
do not print max radius of gyration. If them 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.
---------------------------------------------------------------------------------------------------
but comparing to the older version of this command (e.g. AT1.2):
------------------------------------------------------------------------------------------------
radgyr [out filename] [time interval] [mask]
Calculate the radius of gyration and the maximal distance of an atom from
the center of
geometry considering atoms in mask. The results are dumped to filename if
the keyword
"out" is specified. Thereby, the time between snapshots is taken to be
interval.
------------------------------------------------------------------------------------------------
which description was pretty clear and unambiguous to me, the description
of the actual version is a bit
unclear to me.
Let's assume the common definition of the radius of gyration Rg of given
group of N atoms:
Rg = SQRT ( SUM[(r_i-r_CM)^2]/N )
where r_i is the position vector of the i'th atom, the r_CN is the
position vector
of the center of mass of the given atom group and N is the number of atoms
in the group.
#1
How is then defined "max radius of gyration" of the given set of atoms ?
#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."
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 ?
b)
What does it mean "massweighted" here? It is something like this ?:
Rg_mw = SQRT ( SUM[(w_i*r_i-r_CM)^2]/N )
where w_i = m_i OR m_i/M, m_i is the mass of i'th atom and M = SUM[m_i] ?
Thanks in advance for any comments !
Best wishes,
Marek
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Received on Thu Jul 26 2012 - 10:00:02 PDT
