RE: AMBER: Box dimensions

From: Steve Seibold <>
Date: Fri, 16 Feb 2007 12:12:41 -0500

My density behaves ok. It goes to the expect values of ~1. My volume
goes from 346839 squared Angstroms to 271774 squared angstroms.

The system behaves ok, in the sense there is no oddities in the
energy/force values etc.. or in the structure itself doing this time. My
rmsd is a reasonable value of 0.3 or so.

I just was talking to someone and they told me they found it
unbelievable that the box dimensions should change that much. So, I took
that to mean my system's production run may have been compromised if
they were correct in thinking that such a "large" dimension change to
the correct density was a problem.

Cheers, Steve

-----Original Message-----
From: [] On Behalf
Of Gustavo Seabra
Sent: Friday, February 16, 2007 11:20 AM
Subject: Re: AMBER: Box dimensions

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
> size went from 64 x 64 x 84 to 59 x 59 x 78. Someone made a comment to
> 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 - 06:07:33 PST
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