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
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>>
>
>
>
> --
> ================================ Current Address =======================
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Received on Sat Nov 03 2012 - 15:00:02 PDT
