One of the challenges molecular modelers often face is the lack of real-time feedback when manipulating structures. Whether you’re refining a structure, adjusting a geometry, or exploring potential distortions, waiting for a full simulation step—or hitting “run” dozens of times—can hinder intuition and slow exploration.
SAMSON, the integrative molecular design platform, addresses this with interactive simulations that give you immediate physical feedback as you manipulate atoms manually. This blog post walks you through how to make use of this feature to better understand molecular behavior interactively, based on the Universal Force Field and real-time state updating mechanisms.
Why Interactive Simulations Matter
Interactive simulations let you drag atoms within molecules and immediately see how the rest of the system responds. It’s like poking a molecule and watching how it vibrates, stretches, or deforms in real time—without rerunning simulations. This capability is especially useful for educational purposes, quick hypothesis testing, and dynamic force inspection.
Setting Up Your Interactive Model
You’ll need a molecular system to start. Either drag and drop a structure from the Asset Browser or manually place atoms in the viewport using the Add editor (by default, a carbon atom).
Once your structure is in place, you’ll add a simulator. Press Ctrl + Shift + M (or Cmd + Shift + M on macOS), or use the menu: Edit > Add simulator. Choose:
- Interaction Model: Universal Force Field
- State Updater: Interactive modeling
Then, just click OK.
Seeing It in Action
Start the simulation by clicking Edit > Start simulation or by pressing X. Now you’re in interactive mode.
Select an atom—say, one of the hydrogens in a methane molecule—and drag it. The rest of the molecule reacts according to the rules of physics derived from the force field and the state updater.
Tuning the Experience
The Interactive modeling state updater has several parameters you might want to adjust:
- Step size: the size of each simulation step. Smaller values give smoother results.
- Number of steps: increasing this makes the simulation more “stiff,” causing it to resist large deformations more strongly.
To modify them, select the state updater in the Document view and open the Inspector.
When to Use It
This technique works well for:
- Checking local stability of geometries
- Exploring structural flexibility
- Evaluating molecular strain in newly built systems
- Educational demonstrations of molecular forces
A Note on Structure
Behind the scenes, SAMSON creates a simulator node in the Document view. It includes:
- A structural model: containing your atoms and bonds
- A dynamical model: representing the degrees of freedom
- An interaction model: the force field
- A state updater: updating positions each step
These nodes are synchronized to deliver consistent, physically meaningful feedback as you manipulate your system in real time.
Explore this feature in detail in the Modeling and Simulation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.