Relax One Region, Keep the Rest in Place

A common molecular-modeling problem is that a small region needs adjustment, but minimizing the entire structure could move parts you want to keep fixed. In SAMSON, you can address this by freezing the atoms outside the region of interest, then minimizing the atoms you unfreeze.

This is different from minimizing a selected molecule. When the interactive minimizer is set to work on a selection, it considers the selection’s whole connected component. Selecting one atom in a molecule therefore does not, by itself, limit minimization to that atom or a nearby fragment. To focus on part of a connected molecule, freeze the rest first.

A controlled workflow

1. Choose what to keep fixed. Select the whole molecule, or clear the selection if you want to freeze the whole document.
2. Freeze the current selection. Use Edit > Freeze. Frozen atoms are fixed in place and appear with a dark blue overlay in the viewport.
3. Choose the region to relax. Select the part of the molecule you want to minimize.
4. Unfreeze that region only. Use Edit > Unfreeze while the region is selected. The surrounding frozen atoms stay fixed.
5. Run interactive minimization. Choose Edit > Minimize, or press Z. When you are ready to stop, use the same command or shortcut again.
6. Restore mobility when finished. Select the molecule, or clear the selection, and use Edit > Unfreeze to unfreeze the whole system.

Before starting, check the dark blue overlay: it provides a visual cue for which atoms are frozen. This is especially useful after changing the selection, because freezing and unfreezing apply to the current selection—or, when the selection is empty, to the whole document. Confirming the intended fixed region can help avoid a surprising result.

Two settings that are easy to confuse

The interactive minimizer uses the Universal Force Field (UFF). By default, it minimizes all molecules in the active document. If your goal is to minimize one whole molecule without affecting other molecules, first disable Include all atoms in the document in Interface > Preferences > Editors > Minimize, then select the molecule. Remember that this limits the operation to a connected component; it does not target just a fragment within that component.

For a fragment-level adjustment, freezing is the key distinction: the frozen atoms do not move during minimization, while the selected and unfrozen region can relax. If you need a simulator workflow with a chosen force field and state updater rather than the interactive minimizer, use Modeling and Simulation.

The practical takeaway is simple: use selection to choose a molecule, and use freezing to constrain part of a molecule. Keeping those two jobs separate makes it easier to control what can move and what must stay put.

Read the SAMSON minimization documentation for more details.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.