stre(for stretch) describes a distance between two atoms. It needs only two atomic indices to be given, the order of which is arbitrary.
invrcoordinate (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
invrmay result in better convergence.
benddescribes a bond angle. It requires three atoms to be specified, of which the third one is the atom at the apex.
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.
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, H2CCO, 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
linp. The two coordinates
linc 1 3 2 4and
linp 1 3 2 4(where 1=oxygen, 2=carbon, 3=carbon, 4=hydrogen) would solve the problem.
compdescribes 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. ). 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 (
...). 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.
k ringn 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).
will bring you back to the internal coordinate menu where you can see the new number of internal coordinates in the headline.
Next: Manipulating the Geometry Up: Internal Coordinate Menu Previous: Interactive Definition of Internal Contents Index TURBOMOLE