Re: [AMBER] question of Radius of Gyration

From: Daniel Roe <>
Date: Thu, 4 Jul 2013 11:36:11 -0600


On Thu, Jul 4, 2013 at 5:55 AM, Chinh Su Tran To
<> wrote:
> *radgyr out gag_RoG.dat mass*

You're not specifying an atom mask here, so if you have ions/solvent
in your system these will be included in your radius of gyration
calculation. Without knowing more details of your simulation I can
only speculate, but if you were performing an explicit solvent
simulation with no coordinate wrapping (i.e. iwrap=0) you might expect
the total RoG of the entire system to increase over the simulation
like that.

> => Does that mean here the RadGyr is the average values of all the atoms in
> the model for each time point (sorry but I am also confused about this time
> value, i.e. how long is the interval here!!) ?

RadiusOfGyration = sqrt( SUM[ dxyz^2 * mass ] / totalMass )

where the sum is over all selected atoms and dxyz^2 is the distance
squared from each atom to the center of mass of all selected atoms.
This calculation is performed for every coordinate frame.

> Then in this case, how the MaxRad could be interpreted?

MaxRad is the maximum observed distance during the radius of gyration


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Jul 04 2013 - 11:00:02 PDT
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