AMBER Archive (2006)

Subject: AMBER: format of qusaiharmonic eigenvector file in AMBER7

From: Phineus Markwick (
Date: Tue Feb 07 2006 - 05:10:44 CST

Dear Amberers,

Could somebody provide some insight into the qh-eigenvector file generated
in AMBER7:
The quasih.f program in AMBER7 produces an output file that contains the
quasi-harmonic eigenvectors. The first array (N*3) are the coordinates
of the average structure. After this the eigenvectors are given for each
mode (another
array of N*3 for each mode).

First, as far as I can tell, the lowest mode is a vibrational mode and
not one of
the 6 rotational/translational modes. Is this correct?

Secondly, are the eigenvectors given as
x1, y1, z1, x2, y2, z2, ....., xN, yN, zN
x1, x2, x3, ...., xN, y1, y2, y3, ..., yN, z1, z2, z3, ..., zN

Finally, what are the units of the eigenvectors? Has the mass-weighting
removed or corrected for and is any normalisation used? In other words,
if I calculate
the length of the eigenvector on some atom j, [ sqrt(xj**2 + yj**2 +
zj**2)], in what way is
this value related to the actual amplitude of fluctuation of atom j for
that particular mode?

with best regards,


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