A common molecular-modeling problem is wanting to improve one region without letting the rest of the structure move. For example, you may be editing a local feature and want its surroundings to remain in place while you inspect the result. The interactive minimizer in SAMSON can do this by freezing the atoms you want to keep fixed, then unfreezing only the region you want to minimize.
The key idea is to treat freezing as a boundary-setting step: fixed atoms stay where they are, while the selected, unfrozen part can respond during minimization. This is different from minimizing a single molecule. Selecting one atom and minimizing generally includes the entire connected component containing that atom. To minimize only part of a connected molecule, use the freeze-and-unfreeze workflow below.
A practical workflow
- Decide what must stay fixed. Select the whole molecule, or leave the selection empty if you intend to freeze the whole document.
- Freeze the surrounding structure. Choose Edit > Freeze. Frozen atoms are fixed and their positions stay unchanged during minimization.
- Select the region to relax. Select the atoms in the part of the molecule you want to minimize.
- Unfreeze that selection. Choose Edit > Unfreeze. This unfreezes only the selected atoms, leaving the rest frozen.
- Run the interactive minimizer. Choose Edit > Minimize, or press Z. When you are ready to stop, choose Edit > Minimize again.
- Restore the system. Select the molecule—or clear the selection—and choose Edit > Unfreeze to unfreeze the whole system.
Frozen atoms appear with a dark blue overlay in the viewport. Use that visual cue to check which parts are fixed before starting. One easily missed detail is the meaning of an empty selection: when you click Edit > Freeze with nothing selected, the whole document is frozen. If you meant to freeze just one molecule, select it first.
The interactive minimizer uses the Universal Force Field (UFF), and its options are available in Interface > Preferences > Editors > Minimize. By default, it minimizes all molecules in the active document. If your goal is instead to minimize one molecule without affecting others, disable Include all atoms in the document, select the molecule, and start minimization. That setting is distinct from freezing: selection controls which connected component is considered, while freezing lets you keep part of a connected component fixed.
When to use a simulator instead
Interactive minimization is useful for editing and local adjustments. If you need a simulator workflow with a chosen force field and state updater, use SAMSON’s Modeling and Simulation tools instead. Choosing the right workflow helps avoid treating a quick interactive edit as though it were a complete simulation setup.
For more details, including single-molecule minimization and simulator-based workflows, see the SAMSON minimization documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.