Hi Steve
I am also witnessing similar behavior for my system: it is a GPCR-membrane
system.
I have been running NPT simulation for almost 300ps now and system's Volume
is constantly Decreasing and as expected Density is Increasing. As you
mentioned , in fact my system box size is also constantly decreasing. For my
system, I guess it means that my lipid is packing around the protein and
possibly because of that as well as the huge size of my system (~ 62,000
atoms), the system has not equilibrated yet.
May be in your system, packing of water around your protein has altered the
volume and hence box dimensions.
Can anybody suggest that for NPT equilibration, should the system be
equilibrated until volume and density becomes more or less constant?
Thanks and Best Regards
Akshay
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
Akshay Patny
PhD Candidate (5th Yr.), Computational Chemistry
Department of Medicinal Chemistry, School of Pharmacy
The University of Mississippi
805 College Hill Rd, # 9, Oxford, MS 38655
E-mail: akshay17.olemiss.edu
Phone (O): (662)-915-1286,(M): (662)-801-5496
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-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Gustavo Seabra
Sent: Friday, February 16, 2007 10:20 AM
To: amber.scripps.edu
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?
Gustavo.
On 2/16/07, Steve Seibold <seibold.chemistry.msu.edu> 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 - 06:07:33 PST
