Dear Dr. Ross,
Im sorry for this late question. As you suggested in the previous thread
that it's a need to perform the vacuum dynamics, may I know what this step
is for?
What can I expect from these results? Did you mean to "mess up" somewhat
both the structures before the long runs with solvent?
Im sorry my knowledge is limited and I hate blackbox. I wanna know more
about the process and the meaning behind.
Thank you.
Chinh
On Wed, Jul 10, 2013 at 1:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > On Thu, Jul 4, 2013 at 11:00 PM, Chinh Su Tran To
> > <chinh.sutranto.gmail.com> 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.
>
> Bill
>
> > --
> > -------------------------
> > 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/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 16 2013 - 00:00:02 PDT
