[gmx-users] Constrain boxsize

[Justin Lemkul]

On 3/18/13 1:36 PM, Kieu Thu Nguyen wrote:
> Dear All,
>
> I want to equilibrate a rectangular box. But after running MD 60 ns, the
> system become to be a cubic box mostly. I do not want this happens. Can
> anyone tell me how to constrain the boxsize. In that case, the boxsize has
> fluctuations but remains the same box-type.
>

If the box shape changes drastically, that usually indicates instability in the 
system.  A stable simulation will preserve the original unit cell shape.  There 
is no special way to constrain it to behave as you want it to.  NVT keeps the 
box dimensions fixed, but that doesn't seem to be what you want.

-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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