When working with complex molecular systems, it’s often useful to focus optimization efforts on just a portion of a molecule — for instance, when adjusting a side chain in a protein without disturbing the overall structure. But how do you do that in a precise and interactive way?
SAMSON, the integrative molecular design platform, offers a simple and efficient way to interactively minimize parts of a molecule by freezing the atoms you want to remain unchanged. This can save computation time, reduce unnecessary distortions, and give you better control over your simulations.
Why freeze atoms?
Suppose you’re refining a ligand’s conformation inside a protein binding site. You likely don’t want the protein’s structure to shift each time you adjust the ligand. By freezing the protein and only minimizing the ligand, you can maintain the structural integrity of the system while optimizing the region of interest.
Step-by-step: Minimizing only part of a molecule
Here’s how you can minimize only part of a molecule in SAMSON:
- Select the entire molecule, or leave the selection empty if you want to freeze everything. Learn how to select at this link.
- Go to Edit > Freeze to freeze (i.e., fix) the atoms in the selection. If nothing is selected, freeze applies to the whole document. Frozen atoms appear with a dark blue overlay in the viewport.
- Now, select the atoms you want to minimize.
- Use Edit > Unfreeze to unfreeze the selected atoms. These are now the atoms eligible for energy minimization.
- Click Edit > Minimize (shortcut: Z) to begin interactive minimization using the built-in Universal Force Field (UFF).
- Once you’re satisfied with the structure, click Edit > Minimize again to stop the minimization.
- To return the system to its editable state, click Edit > Unfreeze with the atoms selected, or nothing selected to unfreeze everything.
Visual cues and interactivity
Frozen atoms are easy to spot in the viewport thanks to a dark blue overlay. This makes it convenient to see which parts of the system are free to move and which are fixed, especially when working on dense molecular assemblies.
You can watch a short demonstration of this process below:
Conclusion
Freezing atoms for partial minimization is a very practical tool in molecular modeling. It provides flexibility when dealing with large systems or localized structural refinements. This simple approach can help improve the focus and efficiency of your modeling workflows in SAMSON.
To explore more options, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.