AMBER Archive (2005)

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

From: yipinl_at_umich.edu
Date: Thu Jan 27 2005 - 11:39:46 CST

Hi, Dr. Case,
Thank you very much for your answer and help!

I have one more question for the values of ntb and ntp in the equilibration and
production runs. According to the perl script for removing charge in the water
environment in the tutorial,
equilibration: ntb = 2 and ntp = 1,
but production: ntb = 1 and ntp = 0.

Would you please tell me why in production runs we need to run in a constant
volume condition, but not a constant pressure condition as in the equlibration
condition?

Thank you very much!
Yipin

Quoting "David A. Case" <case_at_scripps.edu>:

> On Wed, Jan 26, 2005, yipinl_at_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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