Re: AMBER: Box dimensions

From: Gustavo Seabra <>
Date: Fri, 16 Feb 2007 11:19:39 -0500

Hi Steve,

How do the density and volume of your system behave? It seems to me
that those properties are actually more important than the box size
itself... When the system relaxes to a determined density (in the cte
P simulation) you would expect the box to change size.

Do you see anything special or suspicious in the general behavior of
the system?


On 2/16/07, Steve Seibold <> wrote:
> Hello Amber
> I have a question about the periodic box dimensions. When I initially run my
> protein in a water box, I run at constant pressure and then after I get to a
> density of 1g/l I run at constant volume. My question involves the
> "shrinkage" in the box dimensions during my constant pressure run. My box
> size went from 64 x 64 x 84 to 59 x 59 x 78. Someone made a comment to me
> about how this size of change is not usually expected. What is the effect on
> my production MD run due to this effect?
> Thanks Steve
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Received on Sun Feb 18 2007 - 06:07:32 PST
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