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From: <yipinl.umich.edu>

Date: Wed, 26 Jan 2005 12:19:43 -0500

Hi, Dr. Case,

Thank you very much for your reply! I have read the tutorial and it is very

helpful. I am a beginner for TI and have some questions for the calculation of

error term in the tutorial:

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+2ô)/n

where n is the number of data points and ô is a correlation length calculated

from the autocrrelation coefficients: ô = sum(1-k/n)ñ, according to the paper

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

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.

Thank you very much!

Yipin

Quoting "David A. Case" <case.scripps.edu>:

*> On Tue, Jan 25, 2005, yipinl.umich.edu wrote:
*

*>
*

*> > Can sander at Amber8/7 do the TI free energy
*

*> > calcualtion with electrostatic decoupling?
*

*>
*

*> There is an example of electrostatic decoupling in the (new) TI tutorial at
*

*> the Amber web site. Basically, you have to do the calculation in two steps,
*

*> manually setting up an electrostatic part and a non-electrostatic part.
*

*>
*

*> ...dac
*

*>
*

*> -----------------------------------------------------------------------
*

*> The AMBER Mail Reflector
*

*> To post, send mail to amber.scripps.edu
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*> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
*

*>
*

*>
*

*>
*

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Received on Wed Jan 26 2005 - 17:53:01 PST

Date: Wed, 26 Jan 2005 12:19:43 -0500

Hi, Dr. Case,

Thank you very much for your reply! I have read the tutorial and it is very

helpful. I am a beginner for TI and have some questions for the calculation of

error term in the tutorial:

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+2ô)/n

where n is the number of data points and ô is a correlation length calculated

from the autocrrelation coefficients: ô = sum(1-k/n)ñ, according to the paper

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

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.

Thank you very much!

Yipin

Quoting "David A. Case" <case.scripps.edu>:

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The AMBER Mail Reflector

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Received on Wed Jan 26 2005 - 17:53:01 PST

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