One common frustration in molecular modeling is the disconnect between model manipulation and immediate feedback. Molecular designers frequently spend time adjusting structures and running batch simulations, only to repeatedly refine parameters through a slow trial-and-error cycle. What if changes could be seen—and felt—in real time?
That’s where SAMSON’s interactive simulation features come in. SAMSON makes it possible to manipulate atoms directly while your system responds under physical laws thanks to its simulator framework. In this blog post, we’ll walk through how to set up and use interactive simulation in SAMSON so you can feel how your molecule behaves as you design it.
What is Interactive Simulation in SAMSON?
Interactive simulations in SAMSON combine a dynamical model, an interaction model (like a force field), and a state updater such as an integrator. This allows you to explore molecular structures in real time—pull an atom, and the rest respond just as they would in reality (or close to it).
This can significantly increase the insight gained per minute spent modeling. You don’t just model structures; you experience their dynamics.
Setting Up Your First Interactive Simulation
To get started:
- Open SAMSON and insert a molecule or atom. For example, use the Add editor to place a carbon atom in the viewport.
- Go to Edit > Add simulator (or use
Ctrl + Shift + Mon Windows/Linux orCmd + Shift + Mon macOS). - For the interaction model, select Universal Force Field (UFF).
- For the state updater, select Interactive modeling.
- Press OK.
The UFF model will compute forces and energies, while the interactive modeling state updater allows SAMSON to respond in real-time as you manipulate atoms.
Start and Stop the Simulation
To begin:
- Click Edit > Start simulation or press
X.
To stop, press the same button or use the same shortcut.
Once started, any movement you apply to atoms will cause a physically-based response from the rest of the molecule, guided by the UFF interaction model and the interactive modeling updater.
Explore the Simulation
Look at your document view. You’ll see a simulator node referencing all the required components: the structural model, the particle system (dynamical model), UFF (interaction model), and interactive modeling updater.
Try selecting an atom (e.g., in a methane molecule) and slowly dragging it. The bonds stretch, neighbors shift—that’s interactive simulation in action. You can control how responsive the system is by adjusting parameters like step size and number of steps in the state updater’s property panel.
For stiffer responses (i.e., system resists deformation more), increase the number of steps. Lower step sizes can result in more precise simulations but reduce responsiveness. It’s all about finding the right balance for your system.
Who Is This For?
This tool can be especially useful for educators, researchers performing quick model evaluations, or anyone iteratively building molecular systems. It not only saves time but helps develop intuition around the behavior of molecular systems.
To dive deeper into interactive modeling and simulation in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/users/latest/modeling-and-simulation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.