Freezing Atoms to Minimize Only Part of a Molecule in SAMSON

When working with large molecular systems, sometimes your goal isn’t to minimize the entire structure. Instead, you may want to refine only a selected part of a molecule, like a side chain in a protein, a ligand in a binding pocket, or a localized defect. This is where partial minimization becomes essential—and SAMSON makes it straightforward by allowing you to freeze atoms.

Freezing atoms in SAMSON means they won’t be moved during minimization. This technique is helpful when you want to maintain the conformation of a large structure while selectively relaxing a fragment of it. For example, you might want to let a flexible region adjust while keeping a rigid core intact.

Why Partial Minimization?

Speed: Reduces computation by focusing only on the region of interest.
Precision: Limits possible distortion of the rest of the system.
Control: Offers more targeted optimization, ideal for simulations or visual refinement.

How to Minimize a Part of a Molecule in SAMSON

Here’s a step-by-step guide to minimizing a specific region of a molecule while keeping the rest untouched:

Select the entire molecule (or leave the selection empty if you want to freeze the entire system).
From the top menu, go to Edit > Freeze. This will freeze the selection—or, if nothing is selected, all atoms in the document.
Select the region you’d like to minimize (e.g., a loop, side chain, or defect site).
Use Edit > Unfreeze to thaw only the selected atoms.
Now, activate the minimization by using Edit > Minimize or pressing Z.
Let the system converge to the local minimum and stop the process with the same command.
Finally, you can unfreeze the entire molecule again by selecting it and using Edit > Unfreeze.

During this procedure, immobile atoms are displayed with a dark blue overlay in the viewport, making it easier to confirm what is frozen and what is active. This visual feedback is particularly useful in complex systems with hundreds or thousands of atoms.

Example of Partial Minimization

Watch the video example below to see this in action. A section of a molecular system is frozen, and a selected part is allowed to relax through energy minimization:

Things to Keep In Mind

The minimizer will treat the selected region as part of the connected component—that is, it will minimize the entire connected network of atoms unless those are frozen.
This method is suitable for small adjustments. For full thermodynamic relaxation, consider using dynamic simulations with force fields and integrators found in the Modeling and Simulation section.

For more details and advanced options, visit the original documentation.

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