AMBER Archive (2009)

Subject: [AMBER] MaxRad ?

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Sat Jun 06 2009 - 15:56:44 CDT

Dear Amber users,

I did "radius of gyration" calculation using ptraj routine from Amber10.

I got 2 outputs "radius of gyration" but also MaxRad.

In AmberTools1.2 manual I found this descrtiption of radgyr command:

----------------------------------------------------
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.
--------------------------------------------------------

I would like just to ensure here about the meaning of the term "center of
geometry".
Does it really mens pure geometrical center ( SUM(r_i)/N ) or it means
"center of mass" ( SUM(r_i*m_i)/SUM(m_i) ) ?
Here N denotes number of atoms within the mask, r_i are position vectors
and m_i masses of that atoms.

Thanks in advance for the information.

Best,

   Marek 

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