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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 4 Jul 2013 11:36:11 -0600

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

Date: Thu, 4 Jul 2013 11:36:11 -0600

Hi,

On Thu, Jul 4, 2013 at 5:55 AM, Chinh Su Tran To

<chinh.sutranto.gmail.com> wrote:

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.

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.

MaxRad is the maximum observed distance during the radius of gyration

calculation.

-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) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jul 04 2013 - 11:00:02 PDT

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