Re: [AMBER] question of Radius of Gyration

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 09 Jul 2013 22:24:33 -0700

Daniel Roe <> wrote:

> Hi,
> 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.
> -Dan

My suggestion on top of Daniel's is to do vacuum dynamics at 100K for
each system, using a distance-dependant dielectric, for a day of CPU,
watch the movies of the results in 3D to convince yourself that the
conformational space is interesting, then build several hydrated models
for each vacuum trajectory, using a sampling of the vacuum dynamic
frames. It might be worth a few days of this rapid feedback, seeing
how temperature or other variables affect the ensemble. Then you can
start the long computer runs with water with a sense that you've chosen
your investment.


> --
> -------------------------
> 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)
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Jul 09 2013 - 22:30:02 PDT
Custom Search