Dragging Atoms, Seeing Molecules React: A Closer Look at Interactive Simulation in SAMSON

One of the most practical challenges in molecular modeling is verifying whether your molecular system behaves as expected during deformation — for example, when an atom is displaced from equilibrium. Traditional simulation setups often involve long preparation workflows and delayed feedback cycles.

In SAMSON, the process becomes more immediate and intuitive thanks to interactive simulation. This feature allows users to manually manipulate atoms and observe the dynamic response of the molecule in real time, without the need for pre-defining long simulation runs or repeatedly exporting frames. It’s feedback-driven modeling — and it can give tremendous insight during early-stage design or hypothesis testing.

What makes it interactive?

In SAMSON, simulations can be configured using simulators that bundle three key components:

  • Dynamical model: degrees of freedom of particles (typically the atoms in your structure)
  • Interaction model: defines the forces in the system (e.g., Universal Force Field)
  • State updater: runs the integration, determining how the system evolves over time (e.g., Interactive modeling)

Once set up, SAMSON enables you to literally drag atoms with your mouse and see how the rest of the molecule responds to this disruption — all while the physical simulation is running.

Getting started with a simple example

Start with a minimal system to explore the setup:

  1. Add a Carbon atom using the Add editor in the left-side menu in the viewport.
  2. Go to Edit > Add simulator (or press Ctrl+Shift+M on Windows/Linux, Cmd+Shift+M on Mac).
  3. Choose Universal Force Field as the interaction model.
  4. Select Interactive modeling as the state updater.
  5. Name the simulator if you like, and press OK.

Add simulator

Click Edit > Start simulation or simply press X. The simulator will now constantly update the atom positions based on the forces in the system. Try selecting an atom and gently dragging it — you’ll see the molecular structure adjusting itself, thanks to the background force field.

Interactive simulation with UFF and interactive modeling state updater

Adjusting the behavior

You’re not limited to the default settings. The step size and the number of steps per frame can be tuned. A higher number of steps can increase the “stiffness” — ideal for mimicking more rigid materials — while increasing the step size may cause stronger or more amplified responses to manipulations. This flexibility lets you experiment and quickly iterate designs, geometries, or interactions.

You can inspect and modify these properties using the Inspector after selecting the simulator in the Document view:

Properties of the UFF interaction model and the Interactive modeling state updater

Useful when?

This functionality is especially helpful when:

  • Testing geometry changes during molecule building
  • Probing flexibility of bonds, rings, or other substructures
  • Creating animations or tutorials for teaching molecular behaviors
  • Initiating conformational searches in intuitive directions

It offers a tactile, visual-first approach to understanding how molecular systems respond to input actions. Because it’s physically based, it yields more meaningful results than static manipulations.

Learn more

If you’re interested in learning more about interactive modeling or want to explore other simulators and force fields, check out the full documentation at 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.

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