A common molecular-modeling problem is that one part of a structure needs adjustment, while the rest should stay exactly where it is. Perhaps a side chain clashes after editing, or a local region needs to settle without disturbing its surroundings. Running minimization on the entire structure can move atoms you intended to preserve.
In SAMSON, one way to handle this is to freeze the atoms you want to keep fixed, unfreeze the region you want to relax, and then run interactive minimization. The key idea is simple: define what must not move before asking the minimizer to adjust anything.
A controlled workflow
- Select the whole molecule, or clear the selection if you want to freeze the whole document.
- Choose Edit > Freeze. This fixes the atoms in the selection—or, if the selection is empty, the atoms in the document.
- Select the part of the molecule you want to adjust.
- Choose Edit > Unfreeze. This makes only the selected atoms free to move again.
- Choose Edit > Minimize to start interactive minimization. When you are done, choose it again to stop.
- Select the molecule or clear the selection, then choose Edit > Unfreeze to unfreeze the rest of the system.
Frozen atoms are not minimized, and their positions remain fixed. In the viewport, they have a dark blue overlay, which helps you check that the intended surroundings are constrained before and during the edit.
Why the selection order matters
Freeze and unfreeze act on the current selection. If you freeze the whole molecule and then unfreeze the region of interest, the surrounding atoms remain fixed while the selected atoms can move. Reversing those steps, or accidentally leaving an unintended selection active, can produce a different set of movable atoms than you planned.
Before starting, take a moment to check the selection and the dark blue frozen-atom overlay. If the wrong atoms are frozen, stop the minimizer and correct the selection state before continuing. When the edit is complete, remember to unfreeze the system if you want to move or edit those atoms normally afterward.
Interactive minimization or a simulator?
The interactive minimizer is intended for hands-on editing: you can move nodes with Move editors or add atoms and assets with the Add editor while minimization is running. Interactive minimization uses the Universal Force Field (UFF).
If you need a simulator workflow with a chosen force field and state updater, use Modeling and Simulation instead. These approaches serve different needs: interactive minimization supports iterative editing, while simulator-based minimization lets you configure a simulation workflow.
One important distinction: by default, the interactive minimizer minimizes all molecules in the active document. If you want to minimize a single molecule rather than the entire document, disable Include all atoms in the document in Interface > Preferences > Editors > Minimize, then select the molecule and start minimization. A selection containing even one atom is treated as its whole connected component for this single-molecule workflow; freezing is the method to use when only part of a molecule should move.
This freeze–unfreeze sequence is useful whenever a local adjustment must respect a fixed molecular context. For the full instructions and related options, see the SAMSON minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.