If you’ve ever needed to adjust only part of a molecular structure while keeping the rest fixed, you’re not alone. This situation arises frequently in structural biology, materials science, and computational chemistry. For example, when refining local geometries around a binding site or studying the mechanical response of a cut carbon nanotube, you may want to minimize only part of your molecule—without affecting the rest.
In SAMSON, this can be achieved using a feature called interactive minimization with frozen atoms. This approach lets you selectively fix (“freeze”) certain atoms, so only specific regions of your model respond to energy minimization steps, guided by the Universal Force Field (UFF).
Why freeze atoms?
A typical pain point when minimizing structures is unintentionally distorting regions that are already in a desirable conformation. Freezing atoms solves this by allowing you to:
- Focus energy relaxation only on regions of interest
- Prevent disruptions in pre-optimized areas
- Study localized structural responses
- Speed up minimization by reducing the number of moving atoms
How it works in SAMSON
To minimize only a part of a molecule using SAMSON’s built-in editor, follow this step-by-step workflow:
- Select the entire molecule or leave the selection empty if you want to freeze all atoms.
- Click Edit > Freeze. This operation freezes all selected atoms—or the whole system if nothing is selected.
- Select the specific part of the molecule you want to minimize.
- Click Edit > Unfreeze. Now, only the atoms in your new selection will be affected by minimization.
- Start the interactive minimization by clicking Edit > Minimize (or press Z).
- Once satisfied, click Edit > Minimize again to stop it.
- If needed, unfreeze the rest of the molecule by selecting frozen atoms and clicking Edit > Unfreeze.
Visual cues and tips
SAMSON provides a convenient visual overlay to help you distinguish frozen atoms. These atoms appear with a dark blue overlay in the viewport, so you can easily track which parts of your structure remain fixed during editing.
This technique is especially useful when exploring conformational strain or testing localized edits. For instance, you can slice a carbon nanotube and watch how just the flexible segment relaxes:
Takeaway
Minimizing only part of a molecule can be key to localized refinement and efficient modeling workflows. SAMSON enables this with a clear, interactive mechanism using freezing and unfreezing operations. This removes the need for manually separating components or relying on external software tools.
This hands-on flexibility makes SAMSON suitable for a wide range of use cases, from quick visual grooming to in-depth molecular mechanics evaluations.
To learn more, visit the full documentation here: https://documentation.samson-connect.net/users/latest/minimizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.