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Description of commands

imet a
This command computes the so-called B -matrix, which is the matrix of the derivatives of the (active and fixed) internal coordinates with respect to Cartesian coordinates. This matrix is used in program relax for the conversion from Cartesian coordinates and gradients to internal ones and vice versa. If this matrix is singular (or even nearly singular) this indicates a linear dependency of your internal coordinate set. As a consequence the geometry update (more exactly the transformation of the updated internal coordinates into Cartesian ones) will fail. This may also happen in the course of a geometry optimization if the coordinates run into linear dependency during their optimization. imet checks the B -matrix and removes linear dependent internal coordinates from your list (their status is changed from #k or #f to #d). If B is only near singular, a warning is issued and the lowest eigenvalue(s) as well as the corresponding eigenvector(s) are displayed. In this case, you should try to find better internal coordinates (although this may not always be possible). After the command imet, there may be too few (active plus fixed) internal coordinates, but certainly not too many (because linear dependencies have been eliminated). Perhaps you will have to add new ones or--better!--try command iaut or ired in the preceding menu.

Command imet should be used always after creating internal coordinates with iaut or idef (especially after iaut, because this command creates usually an overcomplete set of internal coordinates).

idef
idef unfolds a little submenu where you can define internal coordinates manually. The exact procedure of the definition will be described below in a separate section.
ideg a
This command gives you the number of symmetry restricted degrees of freedom (for the atomic set specified by a). Without symmetry, this is just 3N - 6 , where N is the number of atoms, but if there is symmetry, some of these degrees of freedom will violate symmetry and therefore are not valid. For geometry optimizations, only the symmetry allowed degrees of freedom are needed, because the symmetry requirements are imposed anyway. In connection with the optional atomic set a this command can help you to find out, in which part of a complicated molecule internal coordinates are missing, if you fail to get the full number of #ideg (which equals the result of ideg all) for the molecule as a whole.
iaut
iaut tries an automatic definition of internal coordinates. This command relies on an recursive procedure which tries to simplify the molecule as far as possible and then starts the definition of internal coordinates. At present not all molecular topologies are supported, therefore it may happen that no internal coordinates can be assigned to your molecule or at least a part of it. However, for all cases in which an automatic assignment of coordinates is possible, iaut has up to now proved to provide very good internal coordinates. If iaut works for your molecule (and in most non-pathological cases it will) we recommend strongly to use these coordinates, as they may help you to save several cycles in the geometry optimization procedure. After creating internal coordinates with iaut you should always use imet (see above), because iaut may provide an overcomplete set of coordinates. All coordinates which conflict with the molecular symmetry are set to ignore by iaut.
iman a
iman allows you to modify the values of internal coordinates. If you specify a list of atoms a only those internal coordinates which refer to only these atoms will be handled. You will get a list of all (active and fixed) internal coordinates and their current values and you will be able to enter a new value for each of them if you like. Default () keeps the value shown. Be aware that all distances are given in atomic units ( 1 a.u. = 52.9 pm ).
ic i x
This option allows you to change the status of a coordinate, e.g. from active to display or every other combination. The syntax is ic 5 d, if coordinate no. 5 is to be set to display, or ic k d, if all active coordinates are to be set to display.
irem i
This option allows you to delete definitions of internal coordinates from your list. The indices of the internal coordinates always refer to the full list of coordinates including display and ignore coordinates. To make sure you delete the right ones, use disi. Also the indices will immediately change if you delete coordinates. If you want to delete several coordinates, this is therefore done most easily if you delete them in order of descending indices (because deletion of a coordinate has only an effect on the coordinates with higher indices). After choosing the coordinates to be deleted, a list of all coordinates involved will be displayed and you will be asked to confirm deletion.

The syntax is simply irem 5 to delete internal coordinate no. 5 or irem d to remove all `display' coordinates.

Hitting will bring you back to the geometry main menu.
next up previous contents index
Next: Interactive Definition of Internal Up: Internal Coordinate Menu Previous: Internal Coordinate Menu   Contents   Index
TURBOMOLE M