Freezing Atoms to Minimize Just Part of a Molecule

In molecular modeling, it’s not uncommon to need fine-grained control over how parts of a molecule are optimized. Whether you’re modeling a protein undergoing a point mutation, refining a flexible loop while keeping the rest of the structure in place, or investigating small regions of a complex system, you might want to minimize only a part of a molecule.

But here’s the challenge: energy minimization tools typically operate on the whole connected structure. That means if you select a single atom in a molecule, most platforms will minimize the entire connected component. This can be inefficient and even misleading when you want the rest of the structure to stay exactly where it is.

SAMSON, the integrative platform for molecular design, provides a simple but powerful solution to this: freezing atoms.

How to Minimize Only a Part of a Molecule in SAMSON

SAMSON makes it possible to freeze parts of a molecule to prevent them from moving during the interactive minimization. This lets you isolate a specific region for minimization while keeping the rest of the system fixed. Here’s a typical workflow:

  1. Select the whole molecule (or leave the selection empty if you want to freeze the entire scene).
  2. Click Edit > Freeze to freeze the selected atoms. If the selection is empty, this freezes all atoms in the document.
  3. Select the atoms you want to minimize. These are the only parts of the molecule that will be affected by minimization.
  4. Click Edit > Unfreeze to unfreeze the selected atoms.
  5. Click Edit > Minimize to start minimizing only the unfrozen region.
  6. Once you’re done, click Edit > Minimize again to stop the process.
  7. To unfreeze the molecule, select the whole molecule again (or leave the selection empty) and click Edit > Unfreeze.

Frozen atoms will appear with a dark blue overlay in the viewport, making it easy to verify which parts of the molecule are immobilized.

The interactive minimization preferences

This method is especially useful when doing local adjustments, such as refining ligand binding geometries, side-chain orientations, or molecular fragments without introducing distortions to the rest of the model.

To see this process in action, there’s a helpful video example in the documentation showcasing how freezing atoms is used during interactive minimization. The short clip clearly illustrates how isolated structural relaxations are possible without affecting the entire molecular system.

By learning how to freeze and unfreeze atoms interactively in SAMSON, you can gain much more control over structure refinement and ensure your simulations focus on what matters most.

Learn more about interactive minimization with freezing techniques in the SAMSON Minimizing documentation.

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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