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From: Eric Hu <eric.y.hu.gmail.com>

Date: Thu, 14 Apr 2005 17:21:40 -0700

Here we are talking about a small difference between two big numbers

which fluctuate so much that the difference is not significant any

more at each individual snapshot. I agree that the standard error in

the mean is probably more useful from the perspective of statistics

and probability. In this case the SD for PBTOT is 0.22 kcal/mol.

Therefore the PBTOT can be reported as -9.4 +/- 0.2 kcal/mol. What

about the confidence level? I assume that the distribution curve is

really flat...

Eric

On 4/14/05, David A. Case <case.scripps.edu> wrote:

*> On Thu, Apr 14, 2005, Eric Hu wrote:
*

*> > # DELTA
*

*> > # -----------------------
*

*> > # MEAN STD
*

*> > # =======================
*

*> > ELE -14.20 28.32
*

*> > VDW -37.03 7.62
*

*> > INT 0.01 0.02
*

*> > GAS -51.21 32.31
*

*> > PBSUR -4.00 0.76
*

*> > PBCAL 45.81 32.31
*

*> > PBSOL 41.82 31.85
*

*> > PBELE 31.61 9.06
*

*> > PBTOT -9.40 6.93
*

*> > GBSUR -5.75 1.10
*

*> > GB 41.98 27.46
*

*> > GBSOL 36.23 26.85
*

*> > GBELE 27.79 4.27
*

*> > GBTOT -14.99 7.54
*

*> >
*

*> > The data here are not usable since the STD is bigger that the actual
*

*> > value.
*

*>
*

*> Sorry, I don't see where the standard deviations are too high(?). I'm pretty
*

*> sure that MMPBSA is reporting the mean and standard deviation of the
*

*> distribution of values for each snapshot. If you want to estimate the
*

*> standard error in the mean, you would have to divide the STD number by the
*

*> square root of the number of independent samples you have. If the snapshots
*

*> are widely separated in time (by more that a few tenths of a picosecond,
*

*> generally), you can take the number of independent samples to be about equal
*

*> to the number of snapshots.
*

*>
*

*> So, the estimated error in the PBTOT or GBTOT numbers is probably pretty
*

*> small. So, if you had 100 snapshots, the estimated error in the mean value of
*

*> GBTOT or PBTOT would be less than 1 kcal/mol.
*

*>
*

*> (All these are "statistical errors", of course, assuming that you indeed have
*

*> a well equilibrated system. The actual errors, arising from deficiencies in
*

*> the force field, and in the continuum solvent model itself, will generally be
*

*> much larger than this.)
*

*>
*

*> ...dac
*

*>
*

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*

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*>
*

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Received on Fri Apr 15 2005 - 01:53:01 PDT

Date: Thu, 14 Apr 2005 17:21:40 -0700

Here we are talking about a small difference between two big numbers

which fluctuate so much that the difference is not significant any

more at each individual snapshot. I agree that the standard error in

the mean is probably more useful from the perspective of statistics

and probability. In this case the SD for PBTOT is 0.22 kcal/mol.

Therefore the PBTOT can be reported as -9.4 +/- 0.2 kcal/mol. What

about the confidence level? I assume that the distribution curve is

really flat...

Eric

On 4/14/05, David A. Case <case.scripps.edu> wrote:

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Received on Fri Apr 15 2005 - 01:53:01 PDT

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