When working on complex molecular systems, it often happens that you want to optimize only a specific part of a molecule—perhaps just a side chain, a functional group, or a distorted region—without disturbing the rest of the structure. This is particularly important in tasks like active site optimization, docking, or the fine-tuning of experimental models. In SAMSON, the integrative platform for molecular design, there is a clean and controlled way to do just that: partial minimization using frozen atoms.
By freezing part of a structure in SAMSON, you can keep atoms fixed during minimization and focus calculations only where they’re needed. Here’s how this works—and why it might be exactly what you need in your modeling workflow.
Minimizing a Specific Molecular Region
To minimize just a portion of a molecule, follow this approach within SAMSON’s user interface:
- Select the whole molecule you’re working with—or leave the selection empty if you want to target the entire system.
- Freeze atoms using
Edit > Freeze. This will lock the current selection (or the entire system, if nothing is selected). - Select the atoms that you want to remain flexible during minimization.
- Unfreeze those atoms using
Edit > Unfreeze. Now, only these atoms can move. - Minimize the structure by starting the interactive minimization with
Edit > Minimize. - Observe, adjust, and finally stop the minimization when you achieve a satisfactory geometry.
- Optionally, unfreeze the system for further operations by clicking
Edit > Unfreeze.
Frozen atoms are visualized in the viewport with a dark blue overlay, making it easy to track what’s movable and what’s not.
Why This Matters
Selective minimization lets you:
- Preserve the geometry of known or experimental parts of the model
- Reduce computational noise from unnecessary geometry changes
- Focus energy minimization efforts exactly where they matter most
Unlike global minimization, where every atom is allowed to relax (potentially introducing unintended changes), this method gives you precision and control. It’s especially helpful when dealing with macromolecules or simulations built from experimental templates where parts of the system should remain untouched.
Visual Example
Check out this short demo video to see partial minimization in action. In the video, part of a molecule is kept fixed while a selected region undergoes minimization:
To learn more about partial minimization and other options, visit the original documentation page: https://documentation.samson-connect.net/users/latest/minimizing/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.