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

Date: Wed, 26 Jan 2005 21:51:32 -0800

On Wed, Jan 26, 2005, yipinl.umich.edu wrote:

*>
*

*> In the tutorial, a formula:
*

*> [sample-rms]*sqrt[correlation-time/length-of-simulation]
*

*> is used to estimate the expected error in the mean value of DV/DL. My
*

*> understanding is that this is a statistical estimate of the error term. So for
*

*> the correlation-time/length-of-simulation term, should I calculate it using
*

*> (1+2?)/n
*

*> where n is the number of data points and ? is a correlation length calculated
*

*> from the autocrrelation coefficients: ? = sum(1-k/n)?, according to the paper
*

*> by Dr. Pearlman at J. Comp. Chem. 1994, 105?
*

The mail encoding I got made it difficult to read your question. Estimating

the number of "independent samples" as simulation-length/correlation time is

qualitative: depending exactly on how you calculate the autocorrelation of the

<dV/dl> values, this value might better be calculated with an extra sqrt(2) or

so. So, you should treat such estimates with care; a better method is

probably to independently re-do the simulation multiple times.

*>
*

*> For the removing of charge in the vacuum, the tutorial said:
*

*> "Hence, the expected error in the mean is about 0.028 * sqrt[ 0.1/50 ] = 0.001
*

*> kcal/mol. "
*

*> But the RMS fluctuation of DV/DL in the output is 0.0807, not 0.028.
*

My mistake...I copied the wrong number from the output. I'll update the

tutorial with this change.

....thanks...dave case

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Received on Thu Jan 27 2005 - 06:53:00 PST

Date: Wed, 26 Jan 2005 21:51:32 -0800

On Wed, Jan 26, 2005, yipinl.umich.edu wrote:

The mail encoding I got made it difficult to read your question. Estimating

the number of "independent samples" as simulation-length/correlation time is

qualitative: depending exactly on how you calculate the autocorrelation of the

<dV/dl> values, this value might better be calculated with an extra sqrt(2) or

so. So, you should treat such estimates with care; a better method is

probably to independently re-do the simulation multiple times.

My mistake...I copied the wrong number from the output. I'll update the

tutorial with this change.

....thanks...dave case

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Received on Thu Jan 27 2005 - 06:53:00 PST

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