Hi Junica,
> 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.
Which QM package do you want to use. We have most of the major ones:
Gaussian, Gamess, ADF, TeraChem, Q-Chem etc already interfaced into AMBER in
our development version so we may be able to save you reinventing the wheel
here.
> I shall not do any dynamics, this calculation is needed only as an
> energy
> part in subtractive (ONIOM) QM/MM scheme.
Can you not just zero all the VDW terms in the force field before you build
the prmtop file? The VDW interactions would still get calculated, they would
just be zero. Since the QM VDW interactions are implicit within the QM
calculation I believe this would give you the behavior you want. That is
MM-MM VDW and QM-MM vdw zeroed out. Alternatively I have some code, again in
the development version but I could send you a large enough snippet of it
for you to back port it to AMBER 11 that allows you to set a mask for atoms
that should have either their EEL or VDW terms zeroed.
> 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.
Can you write out as an equation exactly which interactions you want, both
inside and outside the cutoff that way I can tell you how best to do it.
This needs to be explicit though, breaking out VDW, EEL and 1-4 VDW and
1-4EEL interactions. You should also break out the link atoms to make sure
those are handled the way you want them to be. Turning off the QM-MM VDW
interaction is fairly simple. Turning off QM-MM and MM-MM would also not be
too hard. I make no claims about performance (since you will have if
statements in inner loops, for the QM-MM VDW case only at least) but it
should be possible to get the interactions you want.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Mon Apr 18 2011 - 08:00:05 PDT
