If you’ve ever tried to manually fine-tune a molecular structure, you know how difficult it can be to predict how atoms should shift when you reposition one of them. Wouldn’t it be helpful if you could visualize forces and relaxations as they happen, in real time? This is precisely what interactive simulations in SAMSON make possible.
Interactive simulation enables you to manipulate atoms—dragging, repositioning—and immediately see how the rest of the molecule responds, guided by physical models such as force fields and integrators. This tool is especially useful during molecular design, geometry optimization, or functionalization of nanostructures, when instant visual feedback can accelerate insight.
Quick Setup for Interactive Simulation
To get started, you just need a molecule in your document. For example, you can:
- Use the Add editor in the left-side panel to simply click and add atoms—Carbon by default.
- Or load a molecule through the Asset Browser.
Once your structure is in place, adding interactivity takes just a few steps:
- Click on Edit > Add simulator or use the shortcut (
Ctrl+Shift+Mon Windows/Linux,Cmd+Shift+Mon Mac). - Choose an interaction model: Universal Force Field.
- Select a state updater: Interactive modeling.
- Click OK.
Behind the scenes, a simulator is formed by linking three components:
- A dynamical model (represents atomic degrees of freedom),
- An interaction model (energy and force calculations), and
- A state updater (numerical integrator, controlling time steps).
Start Simulation and Watch the Molecule Adapt
You’re now ready to explore. Use the shortcut X or click Edit > Start simulation to launch the simulation. Try this:
- Click and drag an atom slowly using your mouse.
- Observe how the other atoms in the molecule respond as if connected by springs—they move into new positions guided by the physics of your simulation.
This immediate feedback reveals structural flexibility and helps spot potential issues (like high strain regions) early in the modeling process. You can also fine-tune how smooth or reactive the deformation feels by adjusting the number of steps or the time step size in the Interactive modeling state updater.
Why Use Interactive Simulation?
Interactive simulations in SAMSON are useful well beyond toy examples. They let you:
- Experiment with new molecule structures on the fly.
- Find local minima interactively before launching heavier geometry optimizations.
- Straighten dangling bonds or poorly aligned fragments quickly.
- Build intuition about molecular response to modifications.
This makes the interactive simulation mode a practical companion to more automated optimization methods, letting you do quick checks and small adjustments without rerunning full calculations.
To learn more, visit the full documentation on Modeling and Simulation with SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.