Relax One Region, Keep the Rest Fixed: A Practical Molecular Modeling Workflow

A common modeling challenge is to improve the geometry of one region without letting the rest of a molecule move. For example, you may want to relax a newly edited section while preserving the surrounding structure as a reference. Minimizing a selection alone may not do what you expect: if you select one atom, SAMSON considers the entire connected component containing that atom. To target part of a molecule, freeze the atoms you want to keep fixed, then unfreeze the region you want to minimize.

This workflow uses SAMSON’s interactive minimizer, which uses the Universal Force Field (UFF). The key is to set the frozen atoms before starting minimization.

Relax only the region you choose

1. Freeze the structure you want to preserve. Select the whole molecule and choose Edit > Freeze. Alternatively, leave the selection empty and choose Edit > Freeze to freeze atoms throughout the document.
2. Select the region to relax. Choose the atoms that should be allowed to move.
3. Unfreeze that selection. Choose Edit > Unfreeze. This unfreezes only atoms in the selection, leaving the other frozen atoms fixed.
4. Start minimization. Choose Edit > Minimize, or press Z. The minimizer adjusts the unfrozen atoms while the frozen atoms stay in their current positions.
5. Stop when ready. Choose Edit > Minimize again. When you want to restore movement to the whole system, select the molecule—or leave the selection empty—and choose Edit > Unfreeze.

Frozen atoms are shown with a dark blue overlay in the viewport. That visual cue is useful before you begin: check that the atoms you intend to hold fixed are marked, and that the region you intend to relax has been unfrozen. If the wrong atoms are mobile, stop the minimizer and correct the frozen state before continuing.

Two selection details worth remembering

First, the default behavior is to minimize all molecules in the active document. If your goal is to minimize a single molecule rather than the entire document, turn off Include all atoms in the document in the Minimize preferences, select the molecule, and start minimization. Even then, a selection containing one atom refers to its whole connected component—not just that atom. Freezing is the method to use when you need to restrict movement to only part of a connected molecule.

Second, freezing fixes positions; it does not mean the frozen region is itself being optimized. The workflow is therefore most useful when you have a region whose geometry should be allowed to adjust while the surrounding atoms remain in place. Keep track of what you freeze and unfreeze, especially when moving between different editing tasks.

When to use a simulator instead

The interactive minimizer is intended for direct editing. If your task calls for a simulator workflow with a force field and a state updater that you choose, use SAMSON’s Modeling and Simulation tools instead. The right approach depends on whether you need an interactive local adjustment or a broader simulation setup.

For the complete instructions and related options, see the SAMSON minimization documentation.

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