[CP2K:1424] Re: Specifying QM/MM system

[Marius Retegan]

Hello
Just two comments on the matter.

On Thu, Oct 9, 2008 at 3:52 PM, Laino Teodoro <teodor... at gmail.com>wrote:

>
> 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.


This is not always possible. One of the reasons that you chose QM/MM is to
eliminate the need for parameters for a certain region of you system (e.g
metalloproteins)

>
> 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.
> run
> 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
> non-bonded.
>

I guess that you refer to van der Waals interactions, since the
electrostatic interaction are computed at a QM level.


>
> Cheers
> Teo
>
>
> 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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