Freezing Atoms to Minimize Just What Matters

When working with complex molecular structures, it’s often important to minimize only a portion of a molecule while keeping the rest intact. This is especially useful when studying local rearrangements, preparing molecules for docking, or refining edited geometries. However, many molecular design tools only allow full-structure minimization, which can distort the rest of the system and introduce unnecessary changes.

This is where freezing atoms in SAMSON becomes helpful. With SAMSON’s interactive minimization feature, you can freeze parts of the molecule you’re not interested in, and focus the minimization where it actually matters.

Freezing Atoms to Minimize a Region

In SAMSON, frozen atoms are excluded from the minimization. Their positions remain fixed during the process, allowing for localized optimization. Frozen atoms are displayed with a dark blue overlay in the viewport, making it easy to visually identify the parts of the molecule that will remain unchanged.

Step-by-Step: Partial Minimization

  1. Select the full molecule or leave the selection empty. (If the selection is empty, actions will apply to the entire document.)
  2. Go to Edit > Freeze to freeze everything currently selected (or everything, if the selection was empty).
  3. Select the region of the molecule you want to minimize.
  4. Go to Edit > Unfreeze to allow minimization only in the selected region.
  5. Use Edit > Minimize (or press Z) to begin interactive minimization.
  6. When done, use Edit > Minimize again to stop.
  7. Finally, to return everything to its editable state, select the molecule (or nothing) and go to Edit > Unfreeze.

This approach is precise and reduces computational overhead. Rather than minimizing the entire system, you can isolate and optimize regions of interest, which is useful in studies involving functional groups, ligand binding sites, or strained parts of large molecules.

The interactive minimization preferences

Tips

  • Frozen atoms don’t move—but they still influence their neighbors. Forces acting on free atoms will still consider interactions with the fixed ones.
  • If you’re doing sequential editing and minimization, freezing can help preserve previously optimized regions.
  • Use this in combination with SAMSON’s selection tools to quickly define exactly what part of a molecule you want to refine.

Check out this short video showing partial minimization of a molecule using frozen atoms, and see the method in action.

To explore more about the interactive minimizer and other related features, visit the full documentation: https://documentation.samson-connect.net/users/latest/minimizing/

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

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