Single Tasks
Single tasks are direct calculations applied to the current working structure.
Energy
Use the energy task when you want a quick numerical evaluation of the current geometry without generating a full optimization pathway.
Typical use cases:
- Compare two edited structures.
- Check whether a manual change is reasonable.
- Screen a structure before a longer workflow.
Geometry optimization
Use optimization when you want MOptima to relax the current structure to a more stable geometry. The Optimization panel combines ordinary and constrained runs. With no atoms selected, Run Optimization relaxes the whole structure normally. Selecting atoms switches the run to constrained optimization. Choose one of four constraint modes: Selected Atom(s), Selected Bond, Selected Angle, or Selected Torsion. Bond, Angle, and Torsion modes require exactly two, three, and four ordered atoms, respectively. The shared selection toolbar above the Editor viewer works here as in every other sidebar panel; its Non-H button can select all non-hydrogen atoms. Batch Optimization always uses ordinary optimization.
In Settings → Advanced, the Constrained optimization row sets the native force constant separately for Distance, Angle, and Torsion in each engine. The defaults are 1 for every mode in both engines. Selected atoms use the Distance column. MMFF94 distance/position values are in kcal/mol/Ų and angle/torsion values in kcal/mol/degree²; GFN2-xTB uses Eh/Bohr².
Both engines optimize the complete current assembly, including interactions between disconnected molecules. Choose MMFF94 for a faster classical force-field optimization or GFN2-xTB for a more computationally expensive semiempirical treatment. Either engine may translate or rotate individual molecules while relaxing the complex.
MMFF94 runs as one continuous minimization. MOptima records the initial structure, one frame every 10 BFGS iterations, and the exact final structure; the result chart uses the real iteration numbers. Single and Batch Optimization use the same recording interval. This does not split or reset the optimizer. GFN2-xTB exposes the frames available from its optimization log. The result curve shows relative energy in kcal/mol, with the lowest recorded point at zero. The axis shows kcal/mol directly with two significant digits; hover a point to see both relative and absolute energy.
Before an xTB optimization, keep every heavy atom in one disconnected molecule at least 2.1 Å from heavy atoms in the others. xTB receives XYZ coordinates, which do not record that the fragments are disconnected. MOptima rejects closer inputs and any result that creates an unrepresented covalent-like contact. If a new bond is intentional, add it in Bond Edit first.
Typical use cases:
- Refine an imported geometry.
- Clean up a manually edited structure.
- Prepare a better starting point for conformer generation or QM setup.
Generate conformers
Use this when you want a broader structural search over accessible conformations.
Generation requires one connected molecule. It is disabled when the ordinary Editor contains a disconnected multi-molecule assembly, because ETKDG conformer generation does not define a reliable intermolecular pose search for that assembly. Energy and Geometry Optimization remain available for the complete assembly. Generated conformers are grouped with Butina clustering; the default RMSD threshold is 1.0 Å.
Reading the output
Single-task results open in result tabs. Keep the Editor tab for manual work and use result tabs to inspect calculated output without losing the active editing context. Clicking the Editor tab always restores the Edit Panel on the left.