One of the most frequent needs in molecular modeling is geometry optimization—adjusting atomic coordinates in order to find a stable molecular structure. But if you’re used to traditional static methods, you might find the interactive approach in SAMSON both efficient and surprisingly responsive.
In SAMSON, geometry optimization is more than a background process. It’s an interactive experience that lets you **see** your molecule relax and adapt in real time. This blog post introduces a quick and effective method to perform molecular geometry optimization using the FIRE (Fast Inertial Relaxation Engine) state updater in SAMSON—a useful tool when you’re working with nanostructures or distorted molecular geometries that need stabilizing.
Solving the Pain of Manual Restoration
If you’ve ever sliced a carbon nanotube only to find yourself spending needless time attempting to patch up the resulting mess, SAMSON’s optimization tools can help restore order instantly. The FIRE state updater, when paired with an interaction model like a force field, finds a local minimum in energy by gradually moving atoms into more favorable positions.
A Simple Use Case: Flattening a Sliced Nanotube
In the following example, a carbon nanotube is sliced—introducing high strain and irregular bonding. Normally, this would require a fair amount of manual adjustment or pre/post-processing in other tools. In SAMSON, however, by applying the FIRE updater, the structure quickly relaxes into a mostly flat graphene sheet.
Watch the process in this brief video:
How It Works
To replicate this in SAMSON, you’ll need:
- A structural model to optimize (e.g., atoms in a nanotube or molecule).
- An interaction model to define the system’s physical properties (e.g., forces, bonds).
- The FIRE state updater.
Once added to your document, the simulator will connect these elements and run the geometry optimization iteratively:
- From the menu, go to Edit > Add simulator.
- Choose the desired interaction model (e.g., Brenner reactive force field).
- Select FIRE as the state updater.
- Press OK to add the simulator.
Now use the shortcut key X (or menu: Edit > Start simulation) to begin optimization. The atomic positions will adjust smoothly as the system searches for a lower energy conformation.
When to Use This
This approach is ideal when you’re building or modifying a model that may have suboptimal geometries—like after removing atoms, creating new bonds, or importing geometries from other sources. It’s particularly handy in nanostructure modeling, such as nanotubes, graphene sheets, or hybrid systems.
Why It’s Worth Sharing
If you’ve spent hours fine-tuning molecular structures by hand or running slow external optimization tools, this streamlined visual process will likely improve your workflow. It also enhances understanding by letting you observe how strain propagates and relaxes under different force field settings.
To learn more about molecular modeling and simulation workflows in SAMSON, visit the full documentation: documentation.samson-connect.net.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from www.samson-connect.net.