A common molecular-modeling problem is that only one region needs adjustment, but minimizing the whole structure can move parts you wanted to keep fixed. The solution is to freeze the surrounding atoms, unfreeze the region you want to relax, and then run interactive minimization. This lets you focus the edit while preserving the rest of the structure’s current positions.
A focused workflow
In SAMSON, interactive minimization uses the Universal Force Field (UFF). To minimize only part of a molecule, follow this sequence:
- Decide what should stay fixed. Select the whole molecule, 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 region to relax. Choose the atoms you want to be able to move.
- Choose Edit > Unfreeze. This unfreezes only the atoms in the current selection.
- Start minimization with Edit > Minimize, or press Z. When you are ready to stop, choose Edit > Minimize again.
- When finished, select the molecule or clear the selection, then choose Edit > Unfreeze to unfreeze the rest of the system.
The order matters: freeze the surroundings first, then unfreeze the part you want to adjust. Frozen atoms are not minimized, and their positions stay fixed. In the viewport, they are shown with a dark blue overlay, which helps you check that the intended context is locked before you begin.
Two selection details that prevent surprises
First, selecting one atom does not necessarily mean that only that atom will be minimized. When minimizing a selection, SAMSON considers the entire connected component containing the selected atom. If that atom belongs to a molecule, the whole connected molecule is included. To restrict movement to a smaller region within that molecule, freeze the molecule and unfreeze only the desired part.
Second, an empty selection has a specific effect when you choose Edit > Freeze: it freezes the whole document. If your goal is to preserve only one molecule while editing another, select the molecule you want to freeze before applying the command. Checking the dark blue overlay is a useful visual confirmation of what is fixed.
When to use this approach
Part-wise minimization is useful when a local edit should be relaxed without changing the surrounding coordinates—for example, when working on a region within a larger structure. During interactive minimization, you can also use Move editors to move nodes or the Add editor to add atoms or assets.
If instead you want to minimize one complete molecule while leaving other molecules untouched, use the separate single-molecule workflow: turn off Include all atoms in the document in Interface > Preferences > Editors > Minimize, select the molecule, and start minimization. Remember that this still includes the molecule’s full connected component.
For a simulator-based workflow where you choose a force field and state updater, use SAMSON’s Modeling and Simulation tools rather than the interactive minimizer. The minimization preferences are available in the Minimize section of the Preferences panel.
For the complete instructions, see the SAMSON minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.