Process Tasks
Source: docs/manual/08-process-tasks.md
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.
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
| Step | What it does |
|---|---|
| Generation | Generates 3D conformers from the current structure using ETKDGv3. The initial pool size (default 1000) controls coverage of conformational space. This step is always first and cannot be removed. |
| Optimization | Geometrically optimizes every conformer in the current pool. Choose MMFF94 for speed or GFN2-xTB for higher accuracy at greater computational cost. GFN2-xTB is slower but produces more reliable relative energies for flexible or heteroatom-rich molecules. |
| Energy Filter | Retains only conformers whose energy lies within a set window above the pool minimum (Threshold mode, in kcal/mol) or simply keeps the N lowest-energy structures (Top N mode). An Optimization step must precede any Energy Filter. |
| Clustering | Groups conformers by 3D structural similarity using Butina clustering with an RMSD threshold (in Å). One representative centroid is kept per cluster. If energies are available, the pool is pre-sorted by energy before clustering so the lowest-energy structure is favored as the centroid. |
Default workflow and rationale
The default pipeline is designed as a two-stage funnel:
- Generation — produce a large initial pool.
- Clustering (loose) — remove obvious geometric duplicates early to reduce the cost of the first optimization.
- MMFF94 Optimization — fast force-field optimization to assign initial energies.
- Energy Filter (threshold) — drop high-energy structures before the expensive xTB step.
- Clustering — remove structures that converged to the same minimum.
- GFN2-xTB Optimization — high-accuracy re-evaluation of the remaining candidates.
- Energy Filter (threshold) — apply a tighter energy window.
- Clustering (tight) — final deduplication at higher accuracy.
- 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.
Reviewing results
After the workflow completes, each surviving conformer is shown as a card with its energy label. 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 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.
Selection rules for scans
The scan coordinate is defined entirely by the atoms you pick and the order in which you pick them. MOptima handles the underlying geometry differently depending on whether the selected atoms are part of a ring.
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.
| Topology | Behavior |
|---|---|
| Acyclic bond | One side of the bond is treated as the moving fragment. All atoms bonded to the second atom (and beyond) translate rigidly along the bond axis. |
| Ring bond | Both atoms are displaced symmetrically in opposite directions by half the requested change, keeping the center of the bond roughly fixed. This avoids unphysical distortion of the ring skeleton. |
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.
| Topology | Behavior |
|---|---|
| All three atoms in the same ring | The vertex atom and its directly bonded substituents outside the ring are translated to satisfy the new angle while keeping atoms 1 and 3 fixed. The slider range is restricted to 60°–240° to stay within physically reasonable bounds. |
| Atoms 1 and 2 in the same ring | Atom 3 and everything beyond it rotate about the axis defined by atom 2. |
| Atoms 2 and 3 in the same ring | Atom 1 and everything beyond it rotate about the axis defined by atom 2. |
| Fully acyclic | Atom 3 and its fragment rotate about the vertex. The slider covers 0°–360°. |
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.
| Topology | Behavior |
|---|---|
| All four atoms in the same ring | A numerical gradient descent solver (crankshaft motion) adjusts side-chain fragments on both sides of the central bond, distributing the angular change across atoms 2 and 3 to avoid breaking ring geometry. |
| Atoms 1, 2, and 3 in the same ring | The central bond axis (2–3) is used to rotate atom 4 and its entire fragment. |
| Atoms 2, 3, and 4 in the same ring | The central bond axis (2–3) is used to rotate atom 1 and its entire fragment. |
| Only atoms 2 and 3 in the same ring | Atom 4 and its fragment rotate about the 2–3 axis. |
| Fully acyclic | The fragment containing atom 3 (and everything beyond) rotates about the 2–3 bond. |
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.