Extensions Menu#

The Extensions menu contains commands for plugins and built-in functions.

Optimize Geometry Ctrl+Alt+O: Optimize the geometry of the current molecule(s) using a Molecular Mechanics Force Field.
Calculate: See Calculate.
Manage Plugins…: Open the Plugin Manager.
Python Settings…: Open a dialog to modify the Python path that Avogadro 2 uses. See Setting Up Python.
User Interface Language…: Open a dialog to switch the language in Avogadro 2.
Yaehmop: Open a submenu that contains features from YAeHMOP (Yet Another extended Hückel Molecular Orbital Package).
Periodic Table: Open an interactive periodic table dialog.

Note

The colorations of each element’s box correspond to the color of each element when drawn.

Open Babel: See Open Babel Interface

Calculate#

The Calculate dropdown contains several functions that calculate properties of the current molecule(s), such as:

Energy: Calculate the energy of the molecule using the currently selected Force Field.
Forces: Calculate the forces in the molecule using the currently selected Force Field.
Configure…: Open the Geometry Optimization configuration dialog. See Configure Dialog
Freeze Selected Atoms: Freeze any selected atoms, such that they do not move when using the Optimize Geometry function.
Freeze X: Freeze the x-coordinate of the selected atom
Freeze Y: Freeze the y-coordinate of the selected atom
Freeze Z: Freeze the z-coordinate of the selected atom
Unfreeze Selected Atoms: Unfreezes any selected atoms, allowing them to move when using the Optimize Geometry function.
Fuse Selected Atoms: Apply constraints to the selected atoms

Note

This will apply varying types of constraints depending on the number of atoms selected. Selecting 2 atoms constrains their distance, selecting 3 atoms constraints distances and the angle between them, and selecting 4 atoms constrains distances, angles, and their dihedral. Selecting 1 atom has no effect.

Unfuse Selected Atoms: Remove constraints that involve the selected atoms.
Constraints…: Open the Constraints dialog. See Constraints Dialog

Configure#

The Configure dialog allows the user to modify some of the parameters relevant to the Force Field optimization, such as the specific Force Field used, the convergence criteria, and the step limit.

Force Field: Select the Force Field that will be used in the Optimize Geometry function.

Note

The selection dropdown is unavailable when the Autodetect box is checked.

Note

The generally available Force Fields are MMFF94, GAFF, UFF, and LJ. Of these, MMFF94 and GAFF are unavailable for charged molecules and radical species.

Constraints#

The constraints dialog allows the user to distance constraints, angle constraints, and dihedral constraints. At the top is a list of the current constraints and the atom indices that those constraints involve.

Add Constraints: Select the type of constraint, the atoms involved in the constraint, and the desired value of the constraint.
Options: Get or delete the constraints of the selected atoms, delete all constraints, or accept the constraints.