Using the Atom Group Editor

The Atom Group Editor, reached via the Atoms Groups item on the main Tools menu, allows you to define subgroups of atoms within a structure for various purposes. It is illustrated below.

ed_frags.tif
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 Atom Group Class 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 Select Atoms and Deselect Atoms items on the Group Actions 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:

Types of Atom Groups

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: Use fragments (atom groups) for generating guess
ONIOM Layer
Define regions using different model chemistries for ONIOM calculations.
Method panel: Multilayer ONIOM Model
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 NMR: compute spin-spin couplings
Select Normal Modes
Specify atoms with which to select normal modes in frequency calculations.
Job Type panel for Frequency or Opt+Freq: Select Normal Modes

The Class Actions 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.