Optimizing Geometry

Avogadro offers several methods to optimize the geometry of your system before further calculations, including the command Extensions ⇒ Optimize Geometry and the interactive AutoOptimize tool.

This section discusses in more detail on the methods used for optimization, use of geometry constraints to control optimization, and generation and use of conformers.

Optimization

• Introduction to Force Fields
  • Lennard-Jones (LJ)
  • UFF
  • MMFF94(s)
  • GAFF
• Geometry Constraints
  • Freezing Atoms
    • Freezing X, Y, or Z Coordinates
    • Fusing Atoms
  • Constrain a Bond or Distance (Two Atoms)
  • Constrain an Angle (Three Atoms)
  • Constrain a Dihedral (Four Atoms)
  • Setting Constraints in Property Windows
• Finding Conformers of Molecules
  • Start with your molecule of interest
  • Optimize Geometry
  • Configure Open Babel Force Fields
  • Set the Conformer Search Options
  • Analyze Results
• Enabling additional force fields
  • Creating an avogadro conda environment
  • Setting the Python path