[gmx-users] equilibrium for box of simulation

[mohammad agha]

Dear Justin,

"my materials are not placed in the smaller box" means if I select box with dimensions 5.99 nm, space is low and insufficient for my molecules! but after equilibrate the box become small.
According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural?

Best Regards
Sara



----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Thursday, October 4, 2012 5:52 PM
Subject: Re: [gmx-users] equilibrium for box of simulation



On 10/4/12 10:06 AM, mohammad agha wrote:
> Dear GROMACS Users,
>
> I asked this question before but I don't understand it!
>
>
> I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and pressure also equilibrate. my question is: is my system and equilibrate mistake, because of reach to smaller box? Is there equilibriums with reach to smaller box?
>
>

What do you mean by "my materials are not placed in the smaller box"?

If a box compresses, it is because the initial configuration was incompatible 
with the desired equilibration conditions and it contracted produce the desired 
quantity (likely pressure).

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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