[gmx-users] equilibrium for box of simulation

[Justin Lemkul]

On 10/4/12 10:38 AM, mohammad agha wrote:
> 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.

Please define what you mean here.  You start with a 6-nm cubic box.  How small 
does it get?  Are the box vectors trending downward, or do they converge?  What 
is the change in density, and is it acceptable?

> According what you said, when the box become smaller in equilibrium, there is not mistake and it is natural?
>

That depends on the magnitude of the change.  Compression indicates that the 
pressure (and thus density of the system) was not at the desired value and the 
system is contracting.  The manner in which the contraction occurs (magnitude, 
speed) is the deciding factor as to whether or not there is a problem.

-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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