For molecular modelers, achieving precise control during a structure’s optimization process represents a crucial challenge. Often, you may want to focus optimization only on certain regions of your molecule while keeping other parts fixed. This level of control can help you simulate complex systems effectively or achieve specific modeling goals. SAMSON makes this task manageable through an interactive minimization process, which includes the ability to minimize only part of a molecule. Here’s how you can do just that.
Freezing and Minimizing a Part of a Molecule
If you aim to optimize a specific section of your molecule, SAMSON’s Freeze feature allows you to exclude other atoms or regions from the process by freezing their positions. The steps below outline how to minimize a part of a molecule efficiently:
- Select the entire molecule or leave the selection empty. This ensures you have the flexibility to isolate the part of the molecule you’re interested in minimizing later.
- Go to Edit > Freeze to freeze (or fix) atoms in the current selection. If no selection is made, the entire molecule or document will be frozen. This step locks any atoms or regions you don’t want involved in the minimization.
- Select the specific part of the molecule that you want to minimize.
- Click Edit > Unfreeze to release only the atoms in the new selection. This means only these atoms will move during the minimization process.
- Start the interactive minimization by selecting Edit > Minimize. Observe how the selected region optimizes while the frozen parts of the molecule remain fixed.
- Once the minimization is complete, stop the interactive minimization by clicking Edit > Minimize again.
- Finally, unfreeze the entire system if needed by selecting the molecule or keeping nothing selected, and clicking Edit > Unfreeze.
An Important Note on Minimization
When minimizing only part of a molecule, it helps to understand SAMSON’s handling of connected components. For example, if you select a single atom, the entire molecule connected to that atom will be considered during the minimization. If your goal is to optimize a specific region only, freeze the areas you want to exclude from the process. Frozen atoms will be marked by a dark blue overlay in the SAMSON viewport.
Why Is This Feature Useful?
This capability is particularly valuable for modelers working on highly specific molecular tasks, such as:
- Optimizing binding regions in protein-ligand complexes without altering the global geometry.
- Fine-tuning parts of a large molecular system for subsequent simulations.
- Simulating structural changes in specific regions while keeping the system stable overall.
The combination of freezing, selective minimization, and SAMSON’s interactive interface ensures that you can control your molecular modeling process with precision and efficiency.
To learn more details about molecular minimization in SAMSON, including other tips and workflows, 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 get SAMSON at https://www.samson-connect.net.