AMBER Archive (2005)

Subject: Re: AMBER: TI with electrostatic decoupling at sander

From: yipinl_at_umich.edu
Date: Wed Jan 26 2005 - 11:19:43 CST

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_at_scripps.edu>:

> On Tue, Jan 25, 2005, yipinl_at_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
>
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