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Specification of available internal coordinates

The following types of coordinates are available:
The stre (for stretch) describes a distance between two atoms. It needs only two atomic indices to be given, the order of which is arbitrary.
The invr coordinate (for inverse r) describes an inverse distance. The declaration is the same as for stre, but in some cases (if you are far away from the minimum) the use of invr may result in better convergence.
bend describes a bond angle. It requires three atoms to be specified, of which the third one is the atom at the apex.
Out-of-plane angle: outp $ a b c d$ is the angle between bond $ a-d$ and plane $ b-c-d$.
Dihedral angle: tors $ a b c d$ is the angle between the planes $ a-b-c$ and $ b-c-d$.
This is a special coordinate type to describe the bending of a near-linear system. linc $ a b c d$ describes the collinear bending of $ a-b-c$ (where the angle is defined as for bend: the apex atom appears last) in the plane of $ b-c-d$ (see also below, command linp). The system $ b-c-d$ has to be non-linear, of course.
This coordinate is similar to linc, but describes the bending of $ a-b-c$ perpendicular to the plane $ b-c-d$. These two types of coordinates are in most cases sufficient to describe the bending of near-linear systems. An example may help you to understand these two coordinate types. Consider ketene, H$ _2$CCO, which contains a linear system of three atoms. Without symmetry, this molecule has 9 degrees of freedom. You could choose the four bond lengths, two CCH angles and the out-of-plane angle of the C-C bond out of the CHH-plane. But then two degrees of freedom still remain, which cannot be specified using these normal coordinate types. You can fix these by using linc and linp. The two coordinates linc 1 3 2 4 and linp 1 3 2 4 (where 1=oxygen, 2=carbon, 3=carbon, 4=hydrogen) would solve the problem.
The type comp describes a compound coordinate, i.e. a linear combination of (primitive) internal coordinates. This is often used to prevent strong coupling between (primitive) internal coordinates and to achieve better convergence of the geometry optimization. The use of linear combinations rather than primitive coordinates is especially recommended for rings and cages (see ref. [20]). Command iaut uses linear combinations in most cases.

After you entered k comp n where n is the number of primitive internal coordinates to be combined, you will be asked to enter the type of the coordinate (stre, bend, ...). Then you will have to enter the weight (the coefficient of this primitive coordinate in the linear combination) and the atomic indices which define each coordinate. The definition of the primitive coordinates is the same as described above for the corresponding coordinate types. It is not possible to combine internal coordinates of different types.

This type helps you to define special ring coordinates. You only have to enter k ring n where n is the ring size. Then you will be asked for the atomic indices of all atoms which constitute the ring and which must be entered in the same order as they appear in the ring. The maximum number of atoms in the ring is 69 (but in most cases the ring size will be limited by the maximum number of atoms which is allowed for define).
Hitting will bring you back to the internal coordinate menu where you can see the new number of internal coordinates in the headline.

next up previous contents index
Next: Manipulating the Geometry Up: Internal Coordinate Menu Previous: Interactive Definition of Internal   Contents   Index