Analysis of Normal Modes in Terms of Internal Coordinates

A general prerequisite for this option is that you have defined a set
of non-redundant coordinates for all 3N-6 (3N-5) degrees of freedom of
your molecule. To make sure that this is the case, you should switch
off redundant coordinates (currently, this is only possible by
manually removing the data group `$redundant` and also removing
the entry `redundant on`

in `$optimize`). Run
`define` to generate non-redundant coordinates by using
the `iaut`

command in the internal coordinate menu (or by
creating them manually via `idef`

). We recommend to use the
`irem`

command first to delete all previous definitions of
internal coordinates. See Section 4 for further details.
If the molecules point group is not *C*_{1}, `define` will set some of
the coordinate to status `d`

(display) or `i`

(ignore). Use
the `ic`

command to change all coordinates to `k`

. You can
also achieve this by editing in the `$intdef` data-group
manually.

The analysis in internal coordinates is switched on by adding a line
in the data-group `$drvopt` that has the following syntax:

`analysis [only] intcoord [print `

`]`

`only`

is added, the program assumes that the file `hessian`

exists and runs only the analysis part of - diagonal elements of the Hessian in internal coordinates (force constants of bonds, angles, etc.) (print level 0)
- complete force constant matrix in internal coordinates (print level 2)
- normal modes in terms of internal coordinates (print level 1)
- Potential energy contributions
, defined as
= *L*_{i}^{n}*L*_{j}^{n}*F*_{ij}/*ω*^{n}

where*L*_{i}^{n}are the elements of the normal coordinate belonging to mode*n*and*F*_{ij}are the elements of the force constant matrix, both expressed in the internal coordinate basis;*ω*is the related eigenvalue. The program will list the diagonal contributions (print level 1), the off-diagonal contributions + = 2 (print level 2 for up to 10 atoms, else print level 10) and the brutto contributions (print level 1). - Based on these quantities, the program will give an assignment of normal modes by listing all internal coordinates with large diagonal or brutto contributions (print level 0).

Note that for large molecules or complicated topologies the B-matrix (that is used to transform from Cartesian coordinates into internal coordinates and vice versa) may become singular. In this case only the normal modes in the internal coordinate basis can be listed.