A common modeling problem is making a local change without letting the rest of a molecule drift. You may want to adjust one group, repair a strained region, or see how a modification settles while keeping the surrounding structure fixed. In SAMSON, the interactive minimizer can do this by freezing the atoms you want to preserve and unfreezing only the atoms you want to relax.
The key distinction is between selecting a molecule and selecting a region within a molecule. By default, the interactive minimizer works on all molecules in the active document. If you want to minimize just one molecule, you can turn off Include all atoms in the document in Interface > Preferences > Editors > Minimize, select that molecule, and start minimization. A selection containing just one atom is not necessarily a request to move only that atom: when minimizing a selection, SAMSON considers the entire connected component. In other words, it can minimize the whole molecule connected to the selected atom.
For a smaller target, freeze the rest of the structure first. This is useful when you want a specific region to move while its molecular surroundings remain in place:
- Select the whole molecule, or leave the selection empty if you want to freeze the whole document.
- Choose Edit > Freeze. The selected atoms—or all atoms if nothing is selected—are fixed.
- Select the part you want to relax.
- Choose Edit > Unfreeze to unfreeze only the atoms in that selection.
- Choose Edit > Minimize to start the interactive minimization.
While minimization runs, you can inspect the structure and, if needed, use the Move editors to move nodes or the Add editor to add atoms or assets. When you are ready to stop, choose Edit > Minimize again. Then 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 have a dark blue overlay, which helps you check which parts are constrained. Before starting, it is worth confirming that the intended target is unfrozen and the surrounding atoms are still frozen. Afterward, remember to unfreeze the system if you plan to continue editing or moving it.
The interactive minimizer uses the Universal Force Field (UFF). If your task calls for a simulator workflow with a chosen force field and state updater, use SAMSON’s simulator-based modeling and simulation tools instead. This distinction helps match the method to the job: interactive minimization is convenient for editing and inspection, while simulator workflows provide choices for a more configured simulation process.
For details on minimization options and related workflows, see the SAMSON minimizing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.