AMBER Archive (2006)

Subject: Re: AMBER: format of qusaiharmonic eigenvector file in AMBER7

From: Chris Moth (chris.moth_at_vanderbilt.edu)
Date: Tue Feb 07 2006 - 08:10:07 CST

Quoting Phineus Markwick <phineus.markwick_at_ibs.fr>:

I am not a guru in this area by any strectch - but I have worked on an upgrade
to mddisplay to display normal modes, and my comments might be helpful. I
hope they do not mislead.

> 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?

I suspect that if you are seeing a largest (> .01) or so eigenvalue in the
bottom 6, you may not be removing translation/rotation from the trajectory.
Our code expects the bottom 6 eigenvalues to be small due to
translation/rotation.

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

yes

> or:
> x1, x2, x3, ...., xN, y1, y2, y3, ..., yN, z1, z2, z3, ..., zN

no

>
> 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?

I work under the assumption that the formatting of the eigenvectors is
exactly like that of the nmode application, which might be a bit better
documented.

In any case of doubt, I think looking directly to the nmode.f and quasih.f
source code is helpful. These programs are quite short.

Chris

>
> with best regards,
> Phin.
>
>
>
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Chris Moth
Vanderbilt University
Email: christopher.moth_at_Vanderbilt.Edu
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