[gmx-users] Constrain boxsize

[Justin Lemkul]

On 3/18/13 9:59 PM, Kieu Thu Nguyen wrote:
> 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 ?
>

I'm not making any recommendation.  You haven't provided nearly enough 
information to do so.  Are the two liquids miscible?  If they are, then the 
outcome you reported before is to be expected.  If they should not mix, then you 
still have a problem.  You need to post a complete description of what you're 
working with, .mdp file(s) used, and ideally links to screenshots that show the 
behavior you are describing.  Without that information, it's largely guesswork 
as to what's really going on.

-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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