Freezing Atoms: A Simple Way to Minimize Only Part of a Molecule in SAMSON

When working with complex molecular structures in SAMSON, one common challenge is how to optimize just a specific region of a molecule without affecting the rest. This need arises frequently—whether you’re focusing on docking sites, local defects, or studying the flexibility of a substructure. Fortunately, SAMSON provides a straightforward mechanism for targeted minimization using atom freezing.

Freezing allows you to keep parts of a molecule static during interactive minimization, enabling local optimization while preserving the overall structure. Here’s how to make use of this helpful feature:

Why Freeze Atoms?

Minimizing a full molecular system when you’re only interested in a small region is inefficient, and potentially harmful if you want the surrounding context to remain unchanged. By freezing parts of your molecule, you avoid unnecessary rearrangements and focus the computational effort on what’s important.

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

Here’s how to minimize only a part of a molecule using SAMSON’s freeze/unfreeze workflow:

  1. Select the entire molecule, or leave the selection empty if you want to freeze the entire document.
  2. Click Edit > Freeze. This freezes all atoms in the current selection or document.
  3. Select the specific atoms you want to minimize.
  4. Click Edit > Unfreeze. Only the selected part is now unfrozen and eligible for minimization.
  5. Click Edit > Minimize (or press Z) to start the minimization. Adjust and observe as needed.
  6. Click Edit > Minimize again to stop minimization.
  7. To restore the molecule’s mobility, select the entire structure (or nothing), and go to Edit > Unfreeze.

During this process, frozen atoms appear with a dark blue overlay in the viewport, making it easier to visually track what’s active.

Visual Example

Curious to see this in action? Here’s a short demonstration showing a nanotube being partially minimized after freezing specific parts:

The interactive minimization preferences

Frozen atoms stay locked in place, allowing selective optimization of the region that matters to your study.

Tips for Precise Control

  • If a single atom is selected, SAMSON minimizes its entire connected component. Be sure to freeze what should remain still before selecting the part to minimize.
  • Useful for modeling conformational changes or refining docking pockets that need local flexibility.

This technique provides a way to model realistic scenarios while retaining geometric context throughout your design process. It’s small, quick to set up, and can make your optimizations much more focused.

To learn more about molecular minimization in SAMSON, including how to minimize full structures and use advanced simulation tools, visit the full documentation page: https://documentation.samson-connect.net/users/latest/minimizing/

SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net

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