[CP2K:1423] Specifying QM/MM system

Laino Teodoro teodor... at gmail.com
Thu Oct 9 13:52:07 UTC 2008

Ciao Ilya,

may I answer your question with an additional provocative question?
Where did you get the starting geometry of your system?
Is it properly thermalized?

The idea behind QM/MM is to have always a fully working MM calculations,
that you can switch to a QM/MM.
You need it for several reasons.. one for all.. you need a  
thermalized structure
and QM/MM is still too far slow to thermalize properly a system (i.e.  
0.1-1 ns of NVT).

So.. I highly suggest you, first, to have a working MM setup.. then  
you can switch
  to QM/MM.

Just to sweep away all the doubts.. charges for QM atoms, though  
requested are
never used. The only classical contribution coming from QM atoms are  
the QM-MM


On 9 Oct 2008, at 14:43, ilya wrote:

> Hi all !!
> I try to make a QM/MM sim of a small molecule (QM part) in a water box
> (MM part). And i have several questions.
> 1. When the program generates connectivity (CONN_FILE_FORMAT GENERATE)
> it also generates connectivity for QM subsystem and asks for bond/
> torsion params, which are not needed for QM part as it is described
> with DFT. So should i specify QM part as ISOLATED_ATOMS to get rid of
> it?
> 2. Even when i use ISOLATED_ATOMS on QM subsys it steel needs charges.
> Do i need to specify them (maybe they are needed for computing
> nonbonded interface QM/MM forces/energies?) or do something else?
> Thanks in advance.
> Ilya.
> >

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