[gmx-users] equilibrium for box of simulation

[Justin Lemkul]

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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