AMBER Archive (2005)Subject: Re: AMBER: big fluctuation in MMPBSA/GA
From: David A. Case (case_at_scripps.edu)
Date: Thu Apr 14 2005  18:33:00 CDT
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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