Freezing Atoms for Targeted Minimization in SAMSON

Interactive energy minimization is one of the most common steps in preparing molecular structures for modeling, especially when repairing imported geometries or refining parts of a system. However, many molecular modelers face the challenge of needing to minimize only a part of a molecule—without affecting the rest of the structure.

If you’re working in SAMSON, there’s a simple and effective way to do just that: freezing atoms.

Why Freeze Atoms?

Let’s say you’ve spent time designing a large molecular structure, and now you need to clean up a newly built substructure—perhaps a ligand you’ve just positioned into a receptor’s binding pocket. Minimizing the full complex could lead to unwanted distortions elsewhere, especially if the force field is sensitive.

Freezing atoms allows you to refine only the portion you’re interested in, while ensuring the rest of the molecule remains fixed in place. This technique gives you control and preserves the integrity of larger systems.

Step-by-Step: Minimizing Only Part of a Molecule

This workflow allows you to interactively minimize only certain atoms in a molecule:

  1. Select Nothing or the Whole Molecule: To start, select nothing, or select the full molecule if you want to be precise.
  2. Freeze the Surrounding Structure: Go to Edit > Freeze. This freezes either the selected atoms or, if nothing is selected, all atoms in the document.
  3. Select the Atoms You Want to Minimize: Choose the specific region of the molecule you’d like to optimize.
  4. Unfreeze the Selected Atoms: These are the only atoms that will be affected by the minimization. Use Edit > Unfreeze.
  5. Start Minimization: Click Edit > Minimize (shortcut: Z) to begin interactive minimization. Observe the motion of the selected atoms while the rest of the structure stays fixed.
  6. Stop Minimization when you’re satisfied with the result by clicking Edit > Minimize again.
  7. Unfreeze Everything if you’d like to enable full structure dynamics again (Edit > Unfreeze).

Interactive minimization preferences

What Happens Under the Hood?

When you freeze atoms, they are excluded from force field updates. In SAMSON’s viewport, frozen atoms appear with a dark blue overlay, making it easy to visualize which components are locked.

This strategy is particularly useful for jobs like:

  • Local refinements of docking poses
  • Fixing clashes introduced during modeling
  • Adjusting ligand side chains or metal centers
  • Testing hypothetical modifications without altering the full system

Video Example

Need a visual walkthrough? Watch this short video that demonstrates the effect of freezing atoms during minimization:

Key Takeaways

  • Freezing atoms allows you to isolate parts of a molecule for minimization.
  • Unfreezing only the atoms of interest ensures targeted optimization.
  • Interactive tuning like this keeps the rest of your system intact.

To learn more about energy minimization workflows in SAMSON, visit the complete 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.

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