Working on Just One Part of a Molecule? Here’s How to Minimize It Without Moving the Rest

When modeling large molecules or complex structures, it’s common to want to tweak and optimize just a small portion without affecting the rest of the system. Whether you’re refining the position of a side chain, adjusting a binding site, or exploring a conformational change, being able to minimize only part of a molecule can be a real time-saver and precision booster.

SAMSON supports this through an intuitive freezing-and-unfreezing mechanism that gives you fine-grained control over which atoms move and which stay fixed. This post walks you through how to do that effectively to isolate the changes you care about.

Why minimize a part instead of the whole?

Full-structure minimizations are useful, but when working on a specific region, minimizing the entire molecule can unintentionally alter regions that should remain unchanged. This can lead to incorrect interpretations or require additional adjustments later.

Step-by-step: Minimizing just what matters

  1. First, select the entire region you’d like to keep fixed. If you don’t select anything, SAMSON will assume you want to freeze everything.
  2. Click Edit > Freeze to lock those atoms in place. They will appear with a dark blue overlay, indicating their frozen state.
  3. Now, select the specific part of the molecule you wish to minimize.
  4. Then, click Edit > Unfreeze to allow only that selection to move.
  5. Click Edit > Minimize to start the interactive minimization process.
  6. Once you’re satisfied with the geometry adjustment, click Edit > Minimize again to stop.
  7. To return everything to a movable state, select the molecule (or keep selection empty) and click Edit > Unfreeze.

What stays fixed vs. what moves

This process uses a physics-based Universal Force Field (UFF) to optimize the atomic positions. Only the unfrozen atoms are affected, meaning their neighbors and the rest of the structure won’t drift or reconfigure. That gives you precision control, especially useful when modifying interfaces or active sites in biomolecules.

Note: Freezing is defined per atom, so you can technically unfreeze even a single atom if needed.

Example in action

The documentation provides a short video example showing this method in use. It clearly visualizes the frozen (blue overlay) atoms and how only the desired portion of a molecule moves during minimization:

The interactive minimization preferences

Final thoughts

This method gives you flexibility and control, allowing you to focus on specific parts of your models while maintaining the integrity of the rest. Before you dive into more global simulations or state updaters, this light-touch minimization can be a helpful first step to test local hypotheses or clean up parts of a structure.

To learn more and explore other minimization techniques and simulation tools in SAMSON, check out the full 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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