AMBER Archive (2005)

Subject: Re: AMBER: small target pressure in constant pressure dynamics

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Thu Apr 14 2005 - 17:26:23 CDT

Maybe I misunderstand the manu (p105) which says "...fluctuations in
the instantaneous pressure on each step will appear to be large
(several hundred bar), but the average value over many steps should be
close to the target pressure..."

Eric

On 4/14/05, Thomas E. Cheatham, III <cheatham_at_chpc.utah.edu> wrote:
>
> > Hi, I am doing a constant pressure simulation of a peptide bound with
> > a protein after a constant volume simulation with Amber 8.0. The
> > average pressure is only 0.6 bar which I believe is considerably low
> > comparing with the target pressure (at 1 bar).
> >
> > ...
> > A V E R A G E S O V E R 5000000 S T E P S
> > NSTEP = 5000000 TIME(PS) = 12020.000 TEMP(K) = 299.96 PRESS = 0.6
>
> Look at the fluctuations in the pressure (and imagine what this would do
> to your ear-drums in real life :-)
>
> > R M S F L U C T U A T I O N S
> > NSTEP = 5000000 TIME(PS) = 12020.000 TEMP(K) = 2.30 PRESS = 215.7
>
> Given the fluctuations, i.e. 0.6+/- 215.7, 0.6 is statistically fairly
> close to 1.0. In such small systems (on the atomic scale), the pressure
> is extremely sensitive to the box size (volume/density). Fluctuations of
> +/- 100 bar are common. If you plot the instantaneous pressure vs. time,
> you will see that it is moving significantly such that 0.6 is a good
> average.
>
>
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