Using the Atom Group Editor
The Atom Group Editor, reached via the item on the main menu, allows you to define subgroups of atoms within a structure for various purposes. It is illustrated below.
The Atom Group Editor
This dialog is used to define fragments and other atoms groups for various types of Gaussian jobs. A separate charge and spin can be optionally assigned to each fragment (as we are doing here). The
popup lists the various kinds of atom groups for which GaussView provides special handling (see below).Note that this dialog serves only to assign atoms to named groups. None of the items here have any effect on the structure or ever remove any atoms from the molecule.
The various columns in the spreadsheet hold the following data:
Once atom groups are defined, the
and items on the menu can be used to select/deselect atoms within an atom group. The other items on this menu have the following uses:There are two other important controls in this dialog:
The defined classes of atom groups are as follows.
Class | Purpose | Gaussian Calculation Setup Use |
---|---|---|
Gaussian Fragment
|
Define atom fragments for use in molecule
specifications, for a fragment guess, and the like.
|
Guess panel:
|
ONIOM Layer
|
Define regions using different model
chemistries for ONIOM calculations.
|
Method panel:
|
Freeze
|
Specify frozen atoms for geometry optimizations.
|
Adds freeze status column to the molecule
specification.
|
NMR Spin-Spin
|
Specify atoms for which to perform spin-spin
coupling calculations during an NMR job.
|
Job Type panel for :
|
Select Normal Modes
|
Specify atoms with which to select normal modes
in frequency calculations.
|
Job Type panel for or :
|
The
menu allows you to create a new type of atom group, to reset the atom group assignments to the default (all in the first group), to remove an atom group class, and to rename a class.