2011/4/18 David A Case <case.biomaps.rutgers.edu>
> On Mon, Apr 18, 2011, Jurica Novak wrote:
>
> > At this stage of my research, solvent I am using is dichloromethane. As
> > stated before, bonding interactions in the "MM" region are 'set' to zero
> by
> > *ibelly* mask allowing only "QM" atoms to move. In that way, bonding
> > interactions in the "QM" region are treated in the spirit of MM
> philosophy.
>
> I don't understand what you mean by the "spirit of MM philosophy". You
> can't
> turn on or off bonding interactions within the QM region.
>
Well, I want to couple Amber with one of quantum chemistry packages to run
QM/MM dynamics with ONIOM electronic embedding scheme. And that's why I have
to have energy term of QM region interacting with MM region *only* by
electrostatic interaction on MM level of theory.
>
> > What I want is to get rid of *all* VDW interactions between *all *atoms
> in
> > MM region and *all* VDW interactions between *all* "QM" and* all* "MM"
> > atoms. All VDW interactions I need to account for are *only* those
> between *
> > all* atoms within "QM" region.
>
> This won't be easy to do, and doesn't make much physical sense. If you
> remove
> vdW interactions between QM and MM atoms, nothing will prevent the QM atoms
> from moving on top of the MM atoms. You results won't have any physical
> meaning, and will probably blow up to boot.
>
I shall not do any dynamics, this calculation is needed only as an energy
part in subtractive (ONIOM) QM/MM scheme.
>
> If you are just interested in a decomposition of (fixed-geometry) energies
> into pieces, why not just ignore (or subtract out) the vdW contribution?
> Note
> that there are no explicit Lennard-Jones terms between QM atoms anyway.
>
There are no explicit Lennard-Jones terms between QM atoms in Amber's QM/MM
scheme, right? But I need calculation on MM level. Labels QM and MM atoms
are used here to highlight which interaction I want to be included and which
not, because of ONIOM scheme for electrostatic embedding.
>
> ....dac
>
>
Thanks,
Jura
>
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Received on Mon Apr 18 2011 - 05:30:04 PDT
