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/acsjpclett.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 Thu Apr 19 2018 - 01:00:02 PDT
