Dear Amber users,
to proceed with my calculations of the reduced mass for each vibrational mode I need to know: when one uses the nmodes() routine, what we get in the vecs file are cartesian coordinates, or mass-weighted cartesian coordinates?
Thank you again,
Lorena
> From: <Lorena.Rosaleny.uv.es>
> Date: Thu, 19 Apr 2018 09:49:05 +0200 (CEST)
> Dear David,
> Thank you for your answer, that was already really helpful!
>> Amber doesn't compute reduced masses for normal modes. I guess you
>> would have to write a script yourself to do this: the masses are in the
>> prmtop file, and the eigenvectors are in the vecs file.
>> Note that cpptraj can read in eigenvector files and work with them.
>> Perhaps that might do what you really want. That is, why do you want to
>> get the reduced mass? (One reason we don't compute these is that I've
>> never needed it, and no one else has ever requested it, as far as I can
remember.)
> I need the reduced mass for the low-energy vibrational modes
> (together with the frequencies and the displacement vectors) in
> order to apply this method: "Determining Key Local Vibrations in
> the Relaxation of Molecular Spin Qubits and Single-Molecule
> Magnets"
> (https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.7b00479).
> For a non-paywalled short live slides presentation (< 4 minutes) of
> the paper:
https://pubs.acs.org/doi/suppl/10.1021/acs.jpclett.7b00479/suppl_file/jz7b00479_liveslides.mp4
> This is precisely what I aim to do at the present moment: to
> determine the key local vibration in the relaxation of a
> metallopeptide-based molecular spin qubit. Actually, the technique
> itself does not have much to do with relaxation or qubits, it's
> simply to relate vibrations with energy differences: what vibration
> is affecting most intensely a given transition.
> I'm new to the computational chemistry world, and it's been a nice
> surprise to get such helpful comments. Thanks again :)
> Lorena
--
Lorena E. Rosaleny Peralvo, Senior Postdoctoral Researcher
Telf. +0034 963 544 418
Instituto de Ciencia Molecular
Universitat de València
c/ Catedrático José Beltrán Martínez nº 2
46980 Paterna (València)
SPAIN
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Received on Mon Apr 23 2018 - 13:00:04 PDT
