[gmx-users] Constrain boxsize

[Kieu Thu Nguyen]

Thank Justin !
I made this rectangular box from merging two cubic boxes. And i carry out
equilibrate this box. Do you mean that i should run NVT, and next step run
NPT, to keep box shape fixed ?

Regards,
~Thu


On Tue, Mar 19, 2013 at 3:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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