In molecular modeling, positioning atoms in the right arrangement isn’t just about visual appeal—it’s critical for making accurate predictions. But achieving a realistic molecular geometry usually requires careful optimization, and this can quickly become a frustrating or time-consuming step if you’re not using the right tools.
Enter interactive geometry optimization in SAMSON: a feature that lets you apply physical force fields and optimization algorithms in real time, meaning you can interactively tweak a structure and watch the molecule respond immediately. Whether you’re slicing cavities in a nanotube or dragging an atom in a small molecule, SAMSON’s modeling engine makes it feel like you’re sculpting atoms with your cursor.
Optimize Geometry Fast with FIRE
One common objective is to relax a molecular structure—i.e., to move atoms into a low-energy conformation. For this purpose, SAMSON supports various state updaters, including the FIRE (Fast Inertial Relaxation Engine) algorithm.
In the example below from the SAMSON documentation, a carbon nanotube is sliced, and the FIRE method is used to relax it. The system automatically collapses to form a mostly flat graphene-like sheet, reflecting physical behavior:
Ready to Try It?
To perform a geometry optimization in SAMSON, start by:
- Adding or loading a molecule.
- Applying a simulator via Edit > Add simulator (Ctrl+Shift+M on Win/Linux or Cmd+Shift+M on macOS).
- Selecting an interaction model such as Universal Force Field (UFF).
- Choosing the FIRE state updater.
- Launching the simulation and watching the geometry optimize in real time.
This setup effectively combines three components: the force field (interaction model), the optimizer (state updater), and the system’s degrees of freedom (dynamical model). You can monitor and tweak these components in the Document view panel.
Small Steps, Big Impact
Modifying a few parameters—like the number of simulation steps or step size in the FIRE updater—can greatly influence how the system behaves. Want a stiffer response? Increase the steps. Want faster feedback? Adjust the step size. This makes SAMSON responsive not only to your models but also to your workflow preferences.
You can even interact with molecules while the simulation runs. Dragging an atom mid-simulation lets you nudge structures into new shapes and immediately see how the system equilibrates. This makes SAMSON especially useful not just for optimization, but also for modeling physically plausible transitions or deformations.
To explore more about simulations and geometry optimization, please visit the official SAMSON Modeling and Simulation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.