Re: Pressure Discrepancy

From: Morad Alawneh (
Date: Fri Apr 20 2007 - 12:30:37 CDT

*Thanks for the explanation.
The expanded graph shows that ACF goes to zero after 1 ps.


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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