One of the key challenges in molecular modeling is ensuring that the geometry of your structure is physically realistic. Whether you’re assembling custom molecules or importing existing ones, minimizing structural strain is essential to avoid artificially high energies and forces. This is where SAMSON’s interactive simulation features can make a big difference — especially when combined with the Fast Inertial Relaxation Engine (FIRE) state updater.
In this post, we’ll look at how to set up and use an interactive simulation in SAMSON to perform geometry optimization. We’ll focus on how you can visually and interactively relax your molecules — not just by launching a calculation, but by guiding it during execution. This allows for a more intuitive modeling process and reflects the flexible nature of working with realistic, dynamic molecular models.
Why you might need it
Let’s say you’re editing a nanotube structure or building a molecule from scratch and you notice improper bond angles or steric clashes. Perhaps you’re combining fragments and need the resulting structure to settle into a stable conformation. Rather than launching a long batch simulation, wouldn’t it be helpful to see the molecule respond to your input directly?
This is exactly what SAMSON allows with the FIRE state updater and a compatible force field such as the Brenner reactive force field. The optimization runs in real time, and you can even manipulate atoms while the simulation is running.
Setting up the optimization
To apply an interactive simulation for geometry optimization in SAMSON:
- Add a structure to the document (for example, a carbon nanotube).
- Go to Edit > Add simulator or use the shortcut
Ctrl+Shift+M(Cmd+Shift+Mon Mac). - As the interaction model, choose a force field. For reactive carbon systems, you might use the Brenner reactive force field.
- For the state updater, select FIRE (Fast Inertial Relaxation Engine).
- Launch the simulation via Edit > Start simulation or pressing
X.
You’ll now see the structure optimize itself in your viewport. If you start from a deformed state (e.g., a sliced carbon nanotube), it will progressively settle into a more relaxed form — like flattening into a graphene sheet.
Customize your simulation
You can fine-tune how your interactive simulation behaves by editing properties of the state updater:
- Modify the step size to adjust how rapidly the system moves toward equilibrium.
- Change the number of steps to control simulation stiffness and responsiveness.
- You can pause and resume the simulation, or even move atoms during the run.
This flexibility not only helps clean up molecular geometries, but it also offers a way to explore how the system behaves under your direct manipulation. It’s especially useful when building or correcting structures that would otherwise require trial-and-error editing.
Watch it in action
This video demonstrates a fast molecular relaxation using the FIRE updater. It shows how a distorted segment of a carbon nanotube flattens into a graphene sheet upon minimization:
This approach can reduce tedious editing, make your structures more chemically realistic, and give you immediate visual feedback. It’s a helpful tool whether you’re preparing systems for simulations, cleaning up geometries, or just playing with molecular ideas.
To learn more, see the full page on modeling and simulation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.