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From: Phineus Markwick <phineus.markwick.ibs.fr>

Date: Tue, 07 Feb 2006 12:10:44 +0100

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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Received on Wed Feb 08 2006 - 06:10:05 PST

Date: Tue, 07 Feb 2006 12:10:44 +0100

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.

-----------------------------------------------------------------------

The AMBER Mail Reflector

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To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Feb 08 2006 - 06:10:05 PST

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