On Mon, Apr 23, 2018, Lorena.Rosaleny.uv.es wrote:
>
> 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?
They are cartesians, not mass-weighted. See the code in
$AMBERHOME/AmberTools/src/sff/nmode.c: look for a comment like:
/* un-mass-weight the eigenvectors: */
Aside: it's good to check that you are interpreting things correctly by
computing V^T * M * V, where M is the (diagonal) mass matrix and V is
the eigenvector matrix. If you've read things correctly, this product
should be a unit matrix.
I've attached a little piece of fortran code that shows how to read
normal modes from ADF, Gaussian, Orca, Jaguar and Amber (all of which
somehow manage to print normal modes in a different format!). The
"check orthonormalization" section was my attempt to stay sane by
ensuring that the vectors I had satisfied the orthonormalization
condition listed above.
...good luck....dac
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Received on Mon Apr 23 2018 - 18:30:03 PDT
