A common modeling frustration: you make a local change, then minimize the structure and discover that parts you wanted to preserve have moved too. The key is to separate two tasks: first, keep the surrounding atoms fixed; then, allow only the region of interest to relax.
SAMSON’s interactive minimizer uses the Universal Force Field (UFF). It can run while you edit, and you can start or stop it with Edit > Minimize or the Z shortcut. For a local minimization, the important step is not just selecting the atoms to optimize. You must also freeze the rest of the structure.
A controlled workflow
- Decide what should stay fixed. Select the whole molecule you want to work on, or leave the selection empty if you intend to freeze the whole document.
- Freeze the surroundings. Choose Edit > Freeze. Atoms in the selection are fixed; if the selection is empty, the whole document is frozen.
- Select the region to relax. Choose the atoms that should be allowed to move.
- Unfreeze only that region. Choose Edit > Unfreeze. This unfreezes atoms in the current selection, while the rest remain fixed.
- Run the minimizer. Choose Edit > Minimize, or press Z. When you are done, choose the same command again to stop the interactive minimization.
- Restore mobility. Select the molecule or leave nothing selected, then choose Edit > Unfreeze to unfreeze the whole system.
Frozen atoms remain in place and are not minimized. In the viewport, they have a dark blue overlay, which gives you a visual check that the intended surroundings are fixed.
Two selection details that prevent surprises
For ordinary single-molecule minimization, selection has a connected-component behavior: selecting one atom does not limit minimization to that atom. SAMSON considers the whole connected component containing it, so the entire molecule is minimized. If the document contains several molecules and you want to minimize just one, turn off Include all atoms in the document in Interface > Preferences > Editors > Minimize, select the molecule, and start minimization.
That setting is different from minimizing just a part of one molecule. For a partial minimization, use the freeze-and-unfreeze sequence above. Think of it as defining a moving region and a fixed environment: freezing establishes the boundary, and unfreezing the selected atoms identifies what may respond.
The image shows the minimization preferences, where you can adjust the interactive minimizer options. By default, the minimizer applies to all molecules in the active document, so it is worth checking this setting when working in a multi-molecule scene.
When to use a simulator instead
The interactive minimizer is useful for immediate editing and local structural cleanup. If your task requires a simulator workflow with a chosen force field and state updater, use SAMSON’s Modeling and Simulation tools instead. The documentation also demonstrates geometry optimization with the FIRE state updater. These approaches serve different workflows: interactive minimization is convenient during editing, while simulator-based minimization lets you choose the simulation components.
For a local change, the practical takeaway is simple: freeze what should not move, unfreeze only the region you want to relax, minimize, and then unfreeze the system when finished. For details and related workflows, see the SAMSON minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.