A common modeling frustration is needing to improve one local region while preserving the surrounding structure. Minimizing the whole system may change parts you intended to leave alone; selecting a single atom, meanwhile, may not give you the small target you expect. In SAMSON, the key is to distinguish which atoms are selected from which atoms are free to move.
This workflow uses freezing to hold the surrounding atoms in place while the region of interest relaxes. It is useful when you want a local adjustment without minimizing the rest of a molecule.
First, know what a selection means
By default, the interactive minimizer works on all molecules in the active document. If you want to minimize just one molecule, first open Interface > Preferences > Editors > Minimize and turn off Include all atoms in the document. Then select the molecule and start minimization with Edit > Minimize (shortcut: Z).
There is an important detail: selecting one atom does not necessarily mean that only that atom—or a nearby fragment—will be minimized. When minimizing a selection, SAMSON considers the whole connected component containing that selection. In a molecule, that can mean the entire molecule. To limit movement to a smaller part, freeze the atoms you want to keep fixed and unfreeze only the target region.
A controlled workflow for a local change
- Decide what must stay fixed. Select the whole molecule, or leave the selection empty if you want to freeze the whole document.
- Freeze the surrounding structure. Choose Edit > Freeze. This fixes the atoms in the selection—or the whole document when nothing is selected.
- Select the region to relax. Select the part of the molecule you want to minimize.
- Free that region. Choose Edit > Unfreeze. Only the selected atoms are unfrozen, so the rest remain fixed.
- Run the interactive minimizer. Choose Edit > Minimize, or press Z. When you are done, use the same command or shortcut to stop it.
- Restore the system. Select the molecule, or clear the selection to address the whole document, and choose Edit > Unfreeze.
Frozen atoms do not participate in the minimization, and their positions stay fixed. In the viewport, frozen atoms have a dark blue overlay. That visual cue is worth checking before you start: it helps confirm that the surroundings you meant to preserve are actually frozen and that the intended region is available to move.
Interactive minimization or a simulator?
The interactive minimizer uses the Universal Force Field (UFF) and is designed for an in-place editing workflow. You can move nodes or add atoms and assets while it is running. If your task instead calls for a simulator workflow with a chosen force field and state updater, use SAMSON’s modeling and simulation tools. The documentation illustrates this alternative with a quick geometry optimization using the FIRE state updater.
These workflows solve different needs: use freezing when you want a specific part to remain fixed during an interactive edit; use a simulator when you need to configure a broader simulation workflow. If you are unsure which atoms will be affected, check the selection setting and the frozen-atom overlay before minimizing.
For the complete instructions, see the SAMSON minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.