From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Mar 28 2007 - 23:07:44 CDT
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?
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
> volume, Å3 box length, Å Average pressure, atm.
> 14706.125 24.5 286.0323
> 14886.936 24.6 63.11659
> 15069.223 24.7 -155.146
> 15160.92188 24.75 -229.526
> 15286.41305 24.8181 -401.745
> 15366.93394 24.8616 -487.346
> He needs to decrease his box size, since his average pressure is
> negative (see my data).
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> ----- 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
> deviation of the mean is larger than the average, you don't have enough
> sampling; if not, then you've got another problem.
> 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*
> The fish are biting.
> Get more visitors
> on your site using Yahoo! Search Marketing.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:09 CST