When working on complex molecular structures, it’s often necessary to refine specific regions without affecting the rest of the molecule. For instance, you might want to optimize the geometry of a functional group or adjust the structure of a specific region while keeping the rest intact. SAMSON provides an incredibly useful feature for this: you can selectively minimize parts of a molecule by freezing atoms, keeping them fixed during the interactive minimization process.
Why Freeze Atoms?
Freezing allows molecular designers to focus their optimization efforts on specific areas, improving efficiency and avoiding unwanted structural changes in other regions. This is particularly important when fine-tuning small sections of a large biomolecule or performing localized adjustments in complex compounds.
The Process of Freezing Atoms
Here’s how you can freeze atoms and minimize parts of a molecule in SAMSON step by step:
- Select the entire molecule (or leave the selection empty if you’d like to consider all the atoms in the molecule).
- Click Edit > Freeze. This fixes the positions of the selected atoms, or if no selection is made, all atoms in the document are frozen.
- Select the specific region or part of the molecule that you would like to minimize.
- Click Edit > Unfreeze. This releases only the selected atoms, making them available for optimization.
- Start the interactive minimization by clicking Edit > Minimize. You’ll see the highlighted region being refined while the frozen sections remain unchanged. Frozen atoms appear with a dark blue overlay in the viewport.
- When the optimization is complete, stop the minimization by clicking Edit > Minimize again.
- To unfreeze all atoms, select the molecule (or leave the selection empty) and click Edit > Unfreeze.
Visual Feedback in SAMSON
One of the strengths of SAMSON’s interactive environment is the visual feedback provided during minimizations. Frozen atoms are clearly marked with a dark blue overlay in the viewport, helping you identify which regions are fixed and ensuring precise editing workflows. Here’s an image of the preferences panel to help you configure this feature:
Minimizing a part of a molecule vs. a single molecule
It’s worth noting the distinction between minimizing just a part of a molecule versus minimizing an entire connected molecule. When only a part of the molecule is unfreezed, SAMSON lets you focus exclusively on that specific region. On the other hand, minimizing an entire molecule optimizes all of its connected atoms. Choosing the appropriate strategy depends on the context and the nature of your simulation work.
For step-by-step instructions and more examples of molecular minimization techniques in SAMSON, please visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.