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.
> 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.
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.
....dac
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Received on Mon Apr 18 2011 - 05:00:02 PDT
