Re: [AMBER] Free energy using MMPBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 30 Aug 2010 11:39:40 -0400

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
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