Hi,
On Thu, Jul 4, 2013 at 5:55 AM, Chinh Su Tran To
<chinh.sutranto.gmail.com> 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
calculation.
-Dan
--
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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
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Received on Thu Jul 04 2013 - 11:00:02 PDT
