Dragging Atoms, Rebuilding Molecules: A Look at Interactive Molecular Simulation in SAMSON

A common challenge in molecular modeling is figuring out how a molecule responds to external constraints or manipulations. What happens when you pull on an atom in a molecule? How does the rest of the structure adapt? Many molecular modelers seek ways to visualize and interact with simulations, instead of waiting for batch jobs to finish. This is where interactive simulations come into play, and in SAMSON, the process is surprisingly practical and smooth.

SAMSON allows real-time interaction with a molecule during a simulation. For example, you can select an atom and drag it while the simulation runs, and the molecule will update its geometry naturally in response. This post walks you through setting up such an interactive simulation using the Universal Force Field (UFF) and the Interactive modeling state updater in SAMSON.

Setting Up the Simulation

Start by adding a molecule, such as methane, via the Asset Browser or the Add editor. If you click in the viewport with the Add editor selected, you’ll place a carbon atom by default.

To add a simulator to this structure:

Click Edit > Add simulator (or use shortcut Ctrl + Shift + M on Windows/Linux or Cmd + Shift + M on macOS).
Select Universal Force Field as the interaction model.
Select Interactive modeling as the state updater.
Optionally name your simulator, then click OK.

You should now see a property window for both the UFF interaction model and the Interactive modeling state updater. These can be reviewed and modified in the Inspector.

Running the Simulation

To start simulating:

Click Edit > Start simulation or hit the X key.
To stop it, hit X again or use the Edit > Stop simulation menu.

The Simulator now appears in the Document view of SAMSON, bundled with its dynamical, interaction, and state updater models.

What Happens When You Move an Atom?

Once the simulation is running, try selecting an atom—say in the methane molecule—and dragging it slowly. You’ll notice an immediate reaction: the rest of the structure dynamically adapts, following molecular mechanics calculated on the fly.

This form of real-time feedback is particularly useful for intuitively exploring molecular geometry, understanding constraints, and designing new configurations manually as you “feel” the system’s response. It’s also easy to tweak simulation parameters—like step size or number of simulation steps—which affects the system’s apparent stiffness and response time.

When This Matters Most

Interactive modeling in SAMSON is especially helpful when working with editable molecular structures, doing education and live demonstrations, or designing components for larger systems. Instead of guessing how a molecule will behave, you can directly trigger movements and watch how the simulation re-balances the structure. In learning contexts, this can be eye-opening for students, offering intuitive insight into molecular flexibility and energy landscapes.

To learn more, please visit the official documentation page.

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