Re: [AMBER] question of Radius of Gyration

From: Daniel Roe <>
Date: Fri, 5 Jul 2013 08:51:38 -0600


On Thu, Jul 4, 2013 at 11:00 PM, Chinh Su Tran To
<> wrote:
> And I got the result as attached. According to the plot, COULD I draw a
> conclusion that the model at the bottom is more stable than the upper one
> regardless their values??

I think the only things these plots tell you is that on average the
top system has a larger radius of gyration than the bottom, and that
the RoG of the starting conformation for the bottom system was closer
to its final value than the top system. It could be that both will
eventually stabilize to different values, or 10 ns from now maybe the
RoG of the bottom system will suddenly spike. In my opinion there's
just too little information at this point to say that either model is
stable. One way to start addressing this would be to start another
independent simulation for each system, using different initial
velocities (and ideally different starting coordinates). Then you can
start to get some idea of the variance in each individual model, which
will help you when you compare the different models to each other.


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 Fri Jul 05 2013 - 08:00:02 PDT
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