AMBER Archive (2005)

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

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Thu Apr 14 2005 - 17:09:18 CDT

> 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.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu