A Practical Guide to Setting Up Interactive Simulations in SAMSON

If you’ve ever wanted to adjust molecular geometries while watching energies and forces respond in real-time, SAMSON‘s interactive simulations offer an intuitive way to do so. But if you’ve never added a simulator before, the process can seem a bit mysterious.

In this post, we’re focusing on one specific task that often confuses new users: how to create and configure a simulator in SAMSON using the Universal Force Field and interactive modeling. This capability is especially useful for researchers and students who want quick, responsive feedback when modifying small molecules, testing geometries, or preparing structures for further simulations.

Why this matters

Many molecular modelers run into a common issue: they build or import a molecular structure, but when they manually distort it—for instance, by dragging an atom—nothing happens. The structure remains frozen, and there’s no sense of how atoms might naturally realign or relax. That’s where a properly configured interactive simulator helps the most. It lets you see in real-time how atoms respond, staying physically meaningful even while you’re manipulating the structure.

Step-by-step: Creating an interactive simulation

Here’s a summary of how to apply a simulator in SAMSON, using the Universal Force Field and interactive modeling as an example:

  1. Create or load a molecule using the Asset Browser or the Add Editor from the left menu (for example, by adding a Carbon atom).
  2. Go to Edit > Add simulator, or use the shortcut Ctrl + Shift + M on Windows/Linux or Cmd + Shift + M on macOS.
  3. In the dialog that appears:
    • Select Universal Force Field as the interaction model.
    • Select Interactive modeling as the state updater.
    • Optionally name your simulator, then press OK.

Add simulator

Running your simulation

Once your simulator is added to the document, you’ll be able to:

  • Start the simulation by clicking Edit > Start simulation or pressing the X key.
  • Stop it again using the same method.

In the Document View, you’ll now see the simulator node connected with an interaction model (this computes forces), a state updater (responsible for evolving the system), and the actual structure. This means dragging an atom won’t just move it; it will naturally affect all surrounding atoms.

Simulator in the document view

Customize your simulation for better control

You can further fine-tune how the system behaves by adjusting parameters of the Interactive modeling updater, such as the number of steps per update and the time step. This flexibility helps you find the right balance between responsiveness and stability.

Try this:

  • Select the “Interactive modeling” updater in the Document view.
  • Open the Inspector and adjust parameters like step size and number of steps.
  • A smaller step size will make movements smoother; increasing the number of steps will simulate a stiffer molecular system.

Properties of the UFF interaction model and interactive updater

Once the simulator is active, try selecting and gently dragging an atom from your molecule. If everything is configured properly, you’ll see the rest of the structure respond dynamically. It’s a simple, visual way to test molecular flexibility and structural logic.

Interactive simulation with UFF and interactive updater

Interactive simulations can save a lot of time when fine-tuning molecules, exploring alternative geometries, or spotting problematic distortions before heavier simulations. This is particularly useful during molecule design, teaching demonstrations, or structural exploration in research projects.

To explore more features and tutorials, consult the SAMSON Modeling and Simulation documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.

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