Optimizing While You Edit#

Most people optimize a structure once they’ve finished building it. The Auto Optimize Tool instead runs the optimization continuously, so the molecule relaxes as you build and move atoms. Drag an atom out of place and watch the rest of the molecule respond; add a group and watch it settle into position.

Start Auto Optimize#

Build or open a molecule. For this example, insert cyclohexane (Build ⇒ Insert ⇒ SMILES… and type C1CCCCC1).
Choose the Auto Optimize Tool from the toolbar, or press Ctrl+7.
In the Tool pane, check the settings:
- Task: Optimize.
- Method: Avogadro suggests a method that works for the elements in your molecule. UFF works across the periodic table; MMFF94 or GAFF are often better for organic molecules. Methods installed as plugins (including machine-learning potentials) appear here too.
Click Start.

cyclohexane with the Auto Optimize Tool pane, method selected and the ΔE overlay visible

The molecule relaxes on screen, and the method and the change in energy (ΔE) are shown in the corner of the view. The optimization keeps running until you click Stop.

Edit While It Runs#

While the optimization is running:

Drag an atom with the left mouse button to pull it to a new position. Release it and the molecule relaxes around the new position. For example, pull one carbon of cyclohexane out of the ring and watch the rest of the ring follow, then settle again when you let go.
Select several atoms first (e.g., with the Selection Tool), then drag with the left mouse button to move them together, or with the right mouse button to rotate them.
Drag in empty space to rotate or zoom the view as usual.

You can also switch to another tool, such as the Draw Tool or Template Tool, while the optimization is still running. Each time you add, delete or change atoms or bonds, Auto Optimize picks up the new structure and keeps relaxing it. Switch back to the Auto Optimize Tool to click Stop.

Tip

This is a fast way to clean up a structure as you draw it: start Auto Optimize, switch to the Draw Tool, and each new atom or group settles into place as you add it.

Hold Parts of the Molecule Fixed#

Auto Optimize respects frozen atoms and constraints:

To keep atoms in place, open Analyze ⇒ Properties ⇒ Atom Properties…, select the rows for those atoms, right-click and choose Freeze Atom.
To keep a distance, angle or dihedral at a fixed value, add a constraint. See Geometry Constraints and Setting a Bond Length, Angle or Dihedral.

This is useful, for example, to relax a ligand while keeping a metal center or a surface fixed.

Watch the Molecule Move: Dynamics#

Set Task to Dynamics to run a short molecular dynamics simulation instead of an optimization. Set the Temperature (in K) and the Timestep (in fs), then click Start. Avogadro first relaxes the structure briefly, then lets it move at the chosen temperature. The current temperature is shown in the corner of the view.

This is a quick way to get a feel for how flexible a molecule is, or to shake a structure out of a strained geometry before optimizing it. It isn’t meant as a replacement for a production simulation.

Note

The steps of a run are combined into a single undo step, so Edit ⇒ Undo takes you back to the structure from before you clicked Start.