Process Tasks

Process tasks generate a series of structures or a workflow result set rather than a single value.

Low-energy conformer search

Use this when your goal is not just diversity, but identification of promising lower-energy candidates.

This workflow requires one connected molecule. The menu action and Run button are disabled for a disconnected multi-molecule assembly. Its first Generation stage uses ETKDG, which does not provide a defined search over relative poses of separate molecules. Use complete-assembly Energy or Geometry Optimization instead when intermolecular interactions are the goal.

The workflow runs a configurable pipeline of steps, each of which takes the conformer pool from the previous stage and transforms it. Each step is shown as a card in the panel and can be reordered, added, or removed. The charge parameter at the top applies globally to any GFN2-xTB step in the pipeline.

Pipeline steps

Default workflow and rationale

The default pipeline is designed as a two-stage funnel:

1. Generation - produce a large initial pool.
2. Clustering - remove geometric duplicates early to reduce the cost of the first optimization.
3. MMFF94 Optimization - fast force-field optimization to assign initial energies.
4. Energy Filter (threshold) - drop high-energy structures before the expensive xTB step.
5. Clustering - remove structures that converged to the same minimum.
6. GFN2-xTB Optimization - high-accuracy re-evaluation of the remaining candidates.
7. Energy Filter (threshold) - apply a tighter energy window.
8. Clustering - final deduplication after the higher-accuracy optimization.
9. Energy Filter (Top N) - limit the output to a manageable number of structures.

You can shorten or extend the pipeline to match the complexity of your molecule and the accuracy you need. For rigid molecules a single MMFF94 optimization and one clustering pass is often sufficient.

Within a supported single-molecule workflow, MMFF94 is the faster classical option and GFN2-xTB provides the semiempirical alternative.

Reviewing results

After the workflow completes, each surviving conformer is shown as a card with its relative energy label. The lowest energy for each available calculation method is 0 kcal/mol; absolute energies remain in the saved project data. Click a card to visualize that conformer in the 3D viewer. Use the Detail button to open a report that summarizes each pipeline step, including the relative energy distribution chart and the structural change at each stage.

PES scan

Use a PES scan when you want to vary a selected bond, angle, or torsion step by step and inspect how the energy changes across that coordinate. MMFF94 and GFN2-xTB both support an optional additional constraint. Without one, the same panel runs an ordinary PES scan.

ScreenshotPES scan result tab showing the scan structure and corresponding energy plot.

Selection rules for scans

The scan coordinate is defined by the atoms you pick and their order. Select exactly two, three, or four atoms for a bond, angle, or torsion scan, respectively, then click Set Scan Coordinate. The saved scan atoms appear in blue in the panel and molecule viewer. MOptima handles geometry changes differently when the atoms are part of a ring.

To keep another part of the structure constrained throughout the scan, use the shared Editor selection toolbar again. Choose Selected Atom(s), Selected Bond, Selected Angle, or Selected Torsion under Additional constraint, select the appropriate atoms, and click Set Constraint. Scan-only atoms appear in blue, constraint-only atoms in gray, and atoms shared by both groups have a small, translucent blue-and-gray marker split into two halves. The split stays visible as you rotate the molecule; clicking either half selects the underlying atom. The Non-H selection shortcut also works for additional atom constraints. The additional constraint keeps its reference from the starting structure throughout every scan step. You cannot fix every scan atom or constrain the same coordinate twice. Clear either saved group with its own button. Changing the structure clears both saved groups.

Each point reports the actual scan coordinate, the target coordinate, and any additional constraint deviation. Scan energy curves use the lowest plotted energy as zero. Energies are evaluated without restraint potentials at each optimized geometry, so the curve represents the underlying MMFF94 or GFN2-xTB energy. The optimized coordinates may differ slightly from their target values because geometry constraints are numerical.

For configured steps larger than 0.05 Å in a bond scan or 5° in an angle or torsion scan, MOptima may prepare intermediate geometries and relax them with constrained MMFF94 before the final optimization. This preparation also runs when the selected final engine is GFN2-xTB. At or below those step sizes, the scan proceeds directly to the selected engine after setting the target geometry.

Settings → Advanced contains separate Distance, Angle, and Torsion force constants for the final scan optimization and for the MMFF94 microstep pre-relaxation before each engine. The native defaults are:

MMFF94 distance values use kcal/mol/Ų and angle/torsion values use kcal/mol/degree². GFN2-xTB scan values use its native Eh/Bohr². An additional geometric restraint uses its own mode's value in MMFF94. xTB has one global force constant per run, so an additional geometric restraint shares the scan coordinate's value. Additional atom restraints use exact fixing and are not affected by k.

Bond scan - select 2 atoms

Pick the two atoms that define the bond you want to stretch or compress. The step size is in Å.

Typical step sizes range from 0.02 Å (fine mapping near equilibrium) to 0.1 Å (coarse survey).

Angle scan - select 3 atoms

Pick three atoms that form the angle. The middle atom (atom 2) is the vertex. The step size is in degrees.

Torsion scan - select 4 atoms

Pick four atoms that define the dihedral 1-2-3-4. The central bond is 2-3. The step size is in degrees.

The torsion scan always expresses the x-axis in continuous, unwrapped degrees so the energy curve remains readable even when the dihedral crosses the ±180° boundary.

Result review

Process tasks usually create richer tabs than single tasks. Review both the structures and the associated values before deciding which geometry should be promoted back into the main workflow.