Re: Pressure Discrepancy

From: Richard Wood (
Date: Fri Apr 20 2007 - 15:23:18 CDT

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 L. Wood, Ph. D.
University of Minnesota
Dept. of Medicinal Chemistry,
College of Pharmacy
717 Delaware St. SE
Minneapolis, MN 55414-2959

----- Original Message ----
From: Morad Alawneh <>
To: Sterling Paramore <>; Prof. David Busath <>
Sent: Friday, April 20, 2007 1:30:37 PM
Subject: Re: namd-l: Pressure Discrepancy


Thanks for the

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


Morad Alawneh

Sterling Paramore wrote:

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.




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




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.





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

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


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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