Dear Marawan,
You've gotten some good advice from Brian and Andreas about how to carry
out the calculation you need.
I would just add that how your carry out and analyse the question depends a
bit on how good you want your IR spectrum to be. If you really want to see
the impact that the solvent has on the IR lineshapes of the solute, and if
your solvent is water, then these are very challenging calculations. You
should be sure to look at a number of papers from Jim Skinner's group at UW
Madison and also Steve Corcelli's group at Notre Dame.
Cheers,
Brent
On Sat, Nov 3, 2012 at 5:33 PM, Andreas Goetz <agoetz.sdsc.edu> wrote:
> Dear Marawan,
>
> As pointed out by Brian, you can obtain an IR spectrum by Fourier
> transformation of the dipole moment autocorrelation function. You can store
> the dipole moment values for the QM region along the trajectory, see the
> AMBER manual. Let me know if you run into problems with this. You will have
> to combine this with the dipole moment in the classical region. I have no
> experience with calculating IR spectra from MD trajectories, but you should
> probably consider a simulation in a water droplet as opposed to a water box
> otherwise you have to use a cutoff for QM-MM electrostatic interactions.
>
> The interface cannot be used for QM/QM multilevel simulations. I would
> follow Brian's suggestions if this is what you are after.
>
> All the best,
> Andy
>
>
> On Nov 3, 2012, at 10:05 AM, Brian Radak wrote:
>
> > Hi Marawan,
> >
> > To get IR spectra, I believe all you need is the time dependence of the
> > dipole moment. I don't know enough about the AMBER/Gaussian interface to
> > say whether or not this is possible, but it doesn't seem unlikely. I
> > believe SQM already supports this at present, although minimal basis set
> > methods (*i.e.* nearly all semiempirical methods) tend not to be accurate
> > in this regard.
> >
> > What you are describing for QM/SQM sounds like an ONIOM type
> calculation. I
> > think the answer will depend strongly on how you want the two regions to
> > interact. Also, Gaussian may already be able to do that kind of
> simulation
> > internally, without needing AMBER. You might want to search through the
> > Gaussian manual or look on a different forum.
> >
> > Regards,
> > Brian
> >
> > On Fri, Nov 2, 2012 at 10:07 PM, marawan hussain
> > <marawanhussain.yahoo.com>wrote:
> >
> >> Dear AMBER users,
> >> I'm asking if it's possible to calculate the IR spectra of small
> molecules
> >> immersed in a water box to calculate the IR vibrational spectra
> employing
> >> the AMBER-Gaussian QM/MM inetrface. The molecule is the QM part which is
> >> handled by Gaussian, the water box is handled by AMBER at the MM level.
> >>
> >> I'm also asking if the inetrface can be used to do QM/SQM for example
> >> Gaussian(B3LYP)/AMBER(DFTB) dynamics.
> >>
> >> Regards
> >> Marawan
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Associate Professor................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Sun Nov 04 2012 - 04:00:02 PST
