A common molecular-modeling frustration is that a structure needs local adjustment, but minimizing the entire model can move regions you wanted to preserve. SAMSON’s interactive minimizer offers a practical way to focus the relaxation: freeze the atoms that should stay fixed, unfreeze the region you want to adjust, and then minimize.
This approach is useful when you want to refine part of a molecule in the context of its current surroundings. The key is to distinguish between selecting a molecule and selecting only the atoms that should move. A selection by itself does not necessarily limit minimization to those atoms.
Why selection alone may not be enough
By default, the interactive minimizer minimizes all molecules in the active document. You can change this behavior in Interface > Preferences > Editors > Minimize by unchecking Include all atoms in the document, then selecting the molecule you want to minimize.
There is an important detail: when minimizing a selection, SAMSON considers the entire connected component containing that selection. In other words, selecting one atom in a connected molecule can result in the whole molecule being minimized—not just that atom or a small region around it.
To minimize only part of a connected molecule, freeze the rest first. This makes the intended moving region explicit and helps avoid accidentally changing atoms outside it.
A focused minimization workflow
- Select the whole molecule you want to work with, or leave the selection empty if you intend to freeze the whole document.
- Choose Edit > Freeze. This fixes the atoms in the selection—or, if nothing is selected, the atoms in the whole document.
- Select the part of the molecule you want to relax.
- Choose Edit > Unfreeze. Only atoms in the current selection are unfrozen.
- Start the interactive minimizer with Edit > Minimize, or press Z. Let the structure adjust, then use the same command or shortcut to stop minimization.
- When you are finished, select the molecule or clear the selection and choose Edit > Unfreeze to unfreeze the rest of the system.
Frozen atoms are not minimized, and their positions stay fixed. In the viewport, they are indicated by a dark blue overlay, which gives you a visual way to check which parts are constrained before and during the workflow.
What the interactive minimizer is—and isn’t
The interactive minimizer uses the Universal Force Field (UFF). While it is running, you can also use Move editors to move nodes or the Add editor to add atoms or assets. These editing actions can be useful when you are adjusting a structure interactively.
If your goal is a simulator-based workflow with a chosen force field and state updater, use Modeling and Simulation instead. That is a different workflow from the quick interactive minimization described here.
The preference panel is also where you can review the minimizer options, including whether all atoms in the active document are included. Checking that setting before you begin is a simple way to avoid minimizing more of the model than intended.
For the complete instructions and related examples, see the SAMSON minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.