QM/MM with isolated QM box

Matt W mattwa... at gmail.com
Sat Feb 20 17:22:14 UTC 2010

Hi Shihao,

it seems that your QM box is much too small  at 6 A^3 , _especially_
if you try to use the MT poisson solver,  it doesn't give the water
molecules room to move.

Use a larger QM box. Why not use the periodic and
decoupling.recoupling scheme, it is bound to end up cheaper?

good luck,


On Feb 21, 1:01 am, shihao <shi... at gmail.com> wrote:
> Hi there,
> I reproduced the error with a smaller system (2 QM water and 21 MM
> water).  When I tried to further reduce the system and use only 1 QM
> water, the simulation worked fine and the QM water travelled freely.
> I've uploaded all the needed files (in qmmm_water_shihao_tar_gz.zip).
> If you run the simulation, you will see that the QM water molecules
> (resid 1 and 2) more or less stay in the YZ plane (which means that
> they could not rotate freely in all directions) after about 200 steps.
> I've also included some result files (dcd, cube, etc.) for your
> convenience.
> Could you give me some clues on whether this is because of some errors
> in my input file or some bugs in the code?
> Many thanks!
> Regards,
> Shihao

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