One further comment, though, is that your snapshots should be sufficiently
uncorrelated, that is you will not learn much about the ensemble binding
free energies if you sample only from a small portion of the total available
states. Long story short, Bill's "rule of thumb" is completely right as
long as those 200 frames are spaced evenly throughout a converged
simulation.
Good luck!
Jason
On Mon, Aug 30, 2010 at 11:29 AM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Honestly, the difference between -138 kcal/mol and -134 kcal/mol does not
> seem that large to me, especially given the difference in the number of
> frames (1 vs. 20) and the error of the MM-PBSA method. Naturally, there
> will
> be some variance in binding energy between each frame, but the binding
> energy will eventually converge with enough frames. I have found that
> usually ~200 frames is sufficient to capture the binding energy using
> MM-PBSA. Using less than 200 frames usually does not sample enough
> conformations to converge the binding energy, and using more than 200
> frames
> does not result in the binding affinity changing any more. Once again, this
> is my experience and results may vary by system, too.
>
> I hope this helps.
>
> -Bill
>
> On Mon, Aug 30, 2010 at 10:12 AM, shenna shearin <smsheari.gmail.com>
> wrote:
>
> > Hello:
> >
> > I am doing a free energy run using MMPBSA on a large system (~116,000
> > atoms). I notice that the more frames I use the lower the free energy
> term
> > gets. I tried running MMPBSA on 1 frame and 20 frames and the
> corresponding
> > free energy values were -138 kcal/mol and -134, respectively. Can someone
> > tell me what is the most amount of frames I should use to get a
> reasonable
> > free energy value?
> > --
> > Shenna
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Aug 30 2010 - 09:00:04 PDT
