Re: [AMBER] pressure not constant

From: case <case.biomaps.rutgers.edu>
Date: Thu, 13 May 2010 07:40:46 -0400

On Thu, May 13, 2010, ashutosh shandilya wrote:

> I have plotted the density vs time graph which seems reasonably stable
> which is with the attachment but still the average pressure is not close to
> 1.0.


> A V E R A G E S O V E R 2500 S T E P S
>
> NSTEP = 500000 TIME(PS) = 2109.000 TEMP(K) = 300.05 PRESS = 0.2

Looks to me like the average pressure *is* close to 1.0; remember that you
have large fluctuations, and are only averaging over 2500 steps. And, as
many others have already pointed out, it's not the pressure that is really
important, but the density -- you want to make sure that the density is
well-equilibrated. Since liquid water is nearly incompressible, the slope of
pressure vs. density is very high, leading to the behavior you observe.

To learn more, consider running some pure water simulations, perhaps at
various temperatures. You can compare your results to literature values,
and it will give you a feeling of what to expect.

....dac


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Received on Thu May 13 2010 - 05:00:06 PDT
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