AMBER Archive (2006)

Subject: AMBER: format of qusaiharmonic eigenvector file in AMBER7

From: Phineus Markwick (phineus.markwick_at_ibs.fr)
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
or:
x1, x2, x3, ...., xN, y1, y2, y3, ..., yN, z1, z2, z3, ..., zN

Finally, what are the units of the eigenvectors? Has the mass-weighting
been
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,
Phin.

 

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