**From:** Richard Wood (*rwoodphd_at_yahoo.com*)

**Date:** Fri Apr 20 2007 - 15:23:18 CDT

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Hi all,

Most interesting in all of this is that the Harris (Daniel Harris), the author of Sterling's analytical chemistry book (which I have also used), is the same Harris as that of the Harris and Bertolucci "Symmetry and Spectroscopy" book.

Good computing,

Richard

Richard L. Wood, Ph. D.

University of Minnesota

Dept. of Medicinal Chemistry,

College of Pharmacy

717 Delaware St. SE

Minneapolis, MN 55414-2959

rwoodphd_at_yahoo.com

----- Original Message ----

From: Morad Alawneh <alawneh_at_chem.byu.edu>

To: Sterling Paramore <paramore_at_hec.utah.edu>; Prof. David Busath <David_Busath_at_byu.edu>

Cc: namd-l_at_ks.uiuc.edu

Sent: Friday, April 20, 2007 1:30:37 PM

Subject: Re: namd-l: Pressure Discrepancy

Thanks for the

explanation.

The expanded graph shows that ACF goes to zero after 1 ps.

Thanks

Morad Alawneh

Sterling Paramore wrote:

Morad,

First of all, you need to expand the autocorrelation graph so that you

can see more precicely how fast it goes to zero (I can't tell from the

graph). Try looking at the range [0:100ps]. Second, according to my

analytical chemistry book (Harris), the student's t for the 95% CI when

you have more than 200 measurements is 1.96, not 2.96. If your mean

Pzz is 5 and the 95% CI really is 10, then it would suggest that the

measured Pzz is statistically indistinguishible from 1 bar and

everything is ok with your simulations. Third, the barostat used in

NAMD works by changing the simulation cell dimensions in a way that the

average pressure hits the target. You have constrained the area to be

constant, so the barostatting mechanism can only work by changing the

simulation cell along the z dimension. If the system was isotropic,

then that would be enough to give the same pressure in every

direction. But since it's a membrane, it is anisotropic and you

shouldn't expect the pressure in the x and y directions to be the same

as the z. If you really want the pressure in the x and y directions to

be 1 bar, then you need to let the area fluctuate as well. However,

that all depends on what you want to do with these simulations.

-Sterling

Morad Alawneh wrote:

*Dear Sterling,

I reported the SE = SD/sqrt(N), so to get 95% CI, we need to multiply

the SE by 2.96. By using 17 as the 95% CI, the 1 bar value for Pzz is

within the range, which is I think what you are looking for. Regarding

the autocorrelation function, see the attachment, it looks the same as

the one for the total pressure. It shows how fast the no correlation

for Pzz. Just to let you know I have printed out the data every 1 ps.

Within the statistical error Pzz is fine, but the total pressure is

not, even I set the pressure to be 1 atm, and that what makes me

confused. You said it is not necessary to expect the total pressure be

the same as the target value, will you explain that to me?

**Unless the target value meant to be for Pzz, then every thing make

sense.*

*

Thanks

Morad Alawneh

*

Sterling Paramore wrote:

What did the decorrelation time for Pzz end

up being in your system? And what confidence interval are you

reporting the standard error at?

Also, you shouldn't necessarily expect the average total pressure to

hit 1 bar exactly (only the zz component) since you used constant area.

-Sterling

On Apr 19, 2007, at 3:05 PM, Morad Alawneh wrote:

*Dear all,

I have here new results to show the pressure problem:

<Pzz> (bar) = 10.93 (+/- 5.75 SE) (+/- 575.24 SD)

<P> (bar) = -33.18 (+/- 3.61 SE) (+/- 361.23

SD)

<V> (A^-3) = 119800.89 (+/- 4.73 SE) (+/- 473.10

SD)

The results show stable average values but away from the target

pressure, which I conclude something is not right about pressure and

any quantity related to pressure should not be trusted until this

problem be figured out.

*

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