**From:** Morad Alawneh (*alawneh_at_chem.byu.edu*)

**Date:** Fri Apr 20 2007 - 12:30:37 CDT

**Next message:**Richard Wood: "Re: Pressure Discrepancy"**Previous message:**hl332_at_drexel.edu: "segmentation fault: Please Help"**In reply to:**Sterling Paramore: "Re: Pressure Discrepancy"**Next in thread:**Peter Freddolino: "Re: Pressure Discrepancy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*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
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*> 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
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*> 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
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*> 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
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*> 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
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*>> 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
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*>> 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
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*>> 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
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*>>>> pressure, which I conclude something is not right about pressure
*

*>>>> and any quantity related to pressure should not be trusted until
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*>>>> this problem be figured out.
*

*>>>> *
*

*>>>
*

*>>>
*

*>
*

- application/pdf attachment: acf_pressure.pdf

**Next message:**Richard Wood: "Re: Pressure Discrepancy"**Previous message:**hl332_at_drexel.edu: "segmentation fault: Please Help"**In reply to:**Sterling Paramore: "Re: Pressure Discrepancy"**Next in thread:**Peter Freddolino: "Re: Pressure Discrepancy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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