**From:** Peter Freddolino (*petefred_at_ks.uiuc.edu*)

**Date:** Wed Mar 28 2007 - 23:07:44 CDT

**Next message:**Hidekazu WATANABE: "It doesn't work with using amber files."**Previous message:**Richard Wood: "Re: Pressure Discrepancy"**In reply to:**Richard Wood: "Re: Pressure Discrepancy"**Next in thread:**Morad Alawneh: "Re: Pressure Discrepancy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This is, of course, precisely the effect that running an NPT

equilibration would have -- given time to equilibrate, you'll end up

with the box size that gives you an average pressure of 1 atm (assuming

that's what you set your pressure at).

Morad, out of curiosity, how did you equilibrate your system prior to

performing your pressure measurements?

Peter

Richard Wood wrote:

*> Hi all,
*

*>
*

*> I still say his box is too big, which is why his presure is too large
*

*> (and negative!).
*

*>
*

*> Here are some numbers from some MD simulations I did in which I varied
*

*> the sides of a cube of water (512 water molecules) and calculated the
*

*> average pressure, the goal of which was to find a box length that gave
*

*> me an average pressure of 1 atm. If I plot the average pressure vs.
*

*> box length, I get a straight line y = -2171.8x + 53499, so an average
*

*> pressure of 1 atm would correspond to my water box being 24.633 A on a
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*> side.
*

*>
*

*> volume, Å3 box length, Å Average pressure, atm.
*

*> 14706.125 24.5 286.0323
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*> 14886.936 24.6 63.11659
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*> 15069.223 24.7 -155.146
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*> 15160.92188 24.75 -229.526
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*> 15286.41305 24.8181 -401.745
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*> 15366.93394 24.8616 -487.346
*

*>
*

*> He needs to decrease his box size, since his average pressure is
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*> negative (see my data).
*

*>
*

*> Richard
*

*>
*

*> Richard L. Wood, Ph. D.
*

*> Computational Chemist
*

*> Cockeysville, MD 21030
*

*> rwoodphd_at_yahoo.com
*

*>
*

*>
*

*> ----- Original Message ----
*

*> From: Sterling Paramore <paramore_at_hec.utah.edu>
*

*> To: Morad Alawneh <alawneh_at_chem.byu.edu>
*

*> Cc: namd-l <namd-l_at_ks.uiuc.edu>
*

*> Sent: Wednesday, March 28, 2007 5:12:06 PM
*

*> Subject: Re: namd-l: Pressure Discrepancy
*

*>
*

*> Try calculating a pressure autocorrelation time. From this, you should
*

*> be able to estimate how many independent pressure observations you made
*

*> over the course of your 10ns simulation. Using that number, you can
*

*> calculate the standard deviation of the mean pressure. If the standard
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*> deviation of the mean is larger than the average, you don't have enough
*

*> sampling; if not, then you've got another problem.
*

*>
*

*> -Sterling
*

*>
*

*> Morad Alawneh wrote:
*

*>
*

*> > *The simulation was for 10 ns with the following SD:
*

*> >
*

*> > Pxx Pyy
*

*> > Pzz Pt P <P>
*

*> > average -105.7232 -119.0253 -16.4359 -112.3742
*

*> > -80.3948 -54.0773
*

*> > SD 516.3578 520.2953 578.8550 395.4912
*

*> > 362.1872 106.7834
*

*> >
*

*> > Thanks.
*

*> >
*

*> > Morad Alawneh*
*

*>
*

*>
*

*>
*

*>
*

*> ------------------------------------------------------------------------
*

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**Next message:**Hidekazu WATANABE: "It doesn't work with using amber files."**Previous message:**Richard Wood: "Re: Pressure Discrepancy"**In reply to:**Richard Wood: "Re: Pressure Discrepancy"**Next in thread:**Morad Alawneh: "Re: Pressure Discrepancy"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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