How to Minimize Just Part of a Molecule in SAMSON Without Affecting the Rest

Interactive molecular minimization is critical in model refinement, but what if you need to relax only a specific region of a large molecule, without moving the rest? This need frequently arises in structure preparation — whether after adding atoms, modifying side chains, or sampling local conformations — and minimizing the whole system could undo intentional configurations or simply take unnecessary compute time.

SAMSON, the integrative molecular design platform, offers a useful solution: the ability to minimize part of a molecule by freezing the rest. This lets you localize geometry optimization and gain better control over your modeling workflow.

Why freeze atoms?

Freezing atoms ensures that they remain fixed during minimization. It’s especially helpful when you’re working on local modifications to a molecule or want to preserve the global shape of macromolecules, such as when docking small ligands into proteins or adjusting specific hydrogen bonds.

Step-by-step: Minimizing a molecular fragment

Here’s how to achieve this in SAMSON:

Select the whole molecule (or keep selection empty to apply globally).
Go to Edit > Freeze to freeze (i.e., fix) the atoms in the selection. If nothing is selected, it freezes all atoms in the document.
Select only the region you would like to minimize — for example, a side chain or fragment.
Click Edit > Unfreeze to unfreeze this selection, allowing only this part to move during minimization.
Start the minimization by clicking Edit > Minimize (or press Z).
When satisfied, stop the minimization via another press of Z or by clicking again on Edit > Minimize.
Finally, unfreeze the full system by selecting the molecule and choosing Edit > Unfreeze.

Frozen atoms are visually marked with a dark blue overlay in the viewport. Only the unfrozen atoms will respond to forces during minimization.

When should you use this?

After making local edits to geometry.
During the refinement of docking poses without affecting the whole protein.
To maintain crystal structure conformation while adjusting hydrogen atoms or side chains.
To explore conformational flexibility in certain regions of polymers or biomolecules.

Watch it in action

Here’s an example from the SAMSON documentation showing a minimization with frozen atoms. The visualization helps understand how only part of the molecule moves while the rest stays rigid.

To learn more about partial or full minimization techniques in SAMSON, refer to their detailed guide:

Minimization Documentation on SAMSON

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.