From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Thu Mar 29 2007 - 08:53:48 CDT
So what concept is it that "we" are not getting?
It doesn't matter what part of phase space you start in (be it the
banana or apple region of phase space), the system will always relax
to become representative of the distribution function. In NPT, the
volume will fluctuate around a value that gives the target average
pressure, regardless of the initial volume. I don't understand why
you refer to the starting value of the volume as the maximum, because
they're not related at all.
-Sterling
On Mar 28, 2007, at 9:33 PM, Richard Wood wrote:
> Hi all,
>
> It seems to me that whether he's running NPT or NVT or bananas, he
> still needs to decrease the STARTING (or maximum, or whatever you
> want to call it) size of his box and let it fluctuate about that
> value.
>
> The name of the algorithm used isn't important, it's the concept
> that is. Not enough of us seem to get that sometimes.
>
> Good calculating,
> 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: Richard Wood <rwoodphd_at_yahoo.com>
> Cc: namd-l_at_ks.uiuc.edu
> Sent: Wednesday, March 28, 2007 11:19:36 PM
> Subject: Re: namd-l: Pressure Discrepancy
>
> But Morad's running in NPT, right? The algorithm is designed so
> that the volume is automatically adjusted to reproduce the desired
> pressure, on average. It could very well be the piston decay time
> giving rise to a very large autocorrelation time (so getting the
> average to be 1atm would require an enormously long simulation
> time). But before you go and run another long simulation, I really
> suggest that you do a quick calculation to determine the pressure
> autocorrelation function.... that'll tell you a lot.
>
> -Sterling
>
>
> On Mar 28, 2007, at 5:23 PM, 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 side.
>>
>>
>> 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
>>
>> 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
>> 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*
>>
>>
>>
>>
>> The fish are biting.
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>
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>
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