Re: AMBER: Pressure Variation for NPT simulation of TIP5P water

From: David A. Case <>
Date: Thu, 22 Nov 2007 09:34:34 -0800

On Thu, Nov 22, 2007, Biman Jana wrote:

> I am doing the NPT simulation of bulk TIP5P water. I am
> using TAUP=0.2 for the equilibration part ( ~ 1.2 ns) and then production
> run at TAUP=2.0 (~1 ns) at 300K. What i find is that the density i am
> getting is somewhat correct but the average pressure is 1.4 instead of
> 1.0. Can anybody tell me where i am going wrong and also any suggestions
> will be highly appreciated.

An average pressure of 1.4 is effectively the same as 1.0. Take a look at the
fluctuations in the pressure. Since water is nearly incompressible, a tiny
change in density leads to a big change in pressure. So, the uncertainty in
the estimate of the mean pressure (especially for only 1 ns of sampling) is


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Received on Sun Nov 25 2007 - 06:07:24 PST
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