Freezing Atoms to Minimize Just Part of a Molecule in SAMSON

When modeling complex molecular systems, it’s common to want to optimize only a specific part of the system—say, a ligand binding site or a reactive region—without altering the rest of the molecule. Re-minimizing the entire structure each time can not only waste time but also potentially move atoms you’d prefer to keep in place.

SAMSON offers a useful feature to handle this situation: you can freeze atoms so that only selected regions of your molecule are minimized. This allows for focused refinements while the rest of your system stays untouched.

Why would you freeze atoms?

There are many scenarios where this is helpful:

  • You want to explore local conformational changes without disturbing a global fold.
  • You’re optimizing a small molecule inside a fixed host, such as a protein active site.
  • You are preparing a patch of a larger system and want to avoid unintentional changes elsewhere.

How to minimize just part of a molecule

Here’s how interactive partial minimization works in SAMSON using the freeze/unfreeze tools:

  1. Initial selection: Select the whole molecule (or leave the selection empty if you want everything frozen).
  2. Freeze: Go to Edit > Freeze. This freezes all currently selected atoms—or everything, if nothing is selected. Frozen atoms will now stay in place.
  3. Select target region: Select the atoms you actually want to minimize.
  4. Unfreeze: Go to Edit > Unfreeze to make just this selection movable again.
  5. Start Minimization: Click Edit > Minimize (or press Z) to begin interactive minimization using the Universal Force Field (UFF).
  6. Stop Minimization: Click again on Edit > Minimize to stop.
  7. Unfreeze everything (optional): At the end, you can unfreeze the system by selecting the full molecule (or nothing) and clicking Edit > Unfreeze.

Frozen atoms are visually distinct in SAMSON—they appear with a dark blue overlay in the viewport. This visual feedback makes it easy to keep track of what parts of your model are passive or active during the minimization process.

Advantages of focused minimization

This workflow is especially useful in iterative molecular design, where you want to systematically study local changes. By freezing everything but the region of interest, you can:

  • Reduce computational cost.
  • Preserve important features of your structure.
  • Experiment with local geometries before broader system changes.

Here’s a visual example from the SAMSON documentation that shows the application of freezing during minimization:

The interactive minimization preferences

Want to learn more on how minimization works in SAMSON, including how to use simulators and the full range of options? Visit the official Minimizing documentation page.

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

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