On Tue, Apr 17, 2018, Lorena.Rosaleny.uv.es wrote:
>
> Finally I got the vecs file with the normal modes on it, and the
> stout_nmodes.txt file. The stdout_nmodes.txt contained basically what
> you posted as output for your "./a.out gcn4p1" execution (I copied most
> of it below). I believe that the reduced masses for each normal mode
> should be in this txt file. How can I find these reduced masses? Thank
> you again,
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.)
....dac
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Received on Tue Apr 17 2018 - 08:00:03 PDT
