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From: David A. Case <case.scripps.edu>

Date: Thu, 14 Apr 2005 16:33:00 -0700

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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Received on Fri Apr 15 2005 - 00:53:00 PDT

Date: Thu, 14 Apr 2005 16:33:00 -0700

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

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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Received on Fri Apr 15 2005 - 00:53:00 PDT

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