Dragging Atoms to Simulate Molecular Behavior in Real Time

Modeling molecular systems traditionally relies on preparing static structures, launching simulation jobs, and then reviewing results afterward. But what if you could “grab” an atom in a molecule and instantly see how it moves and how the entire system responds?

SAMSON’s real-time, interactive simulation capabilities make this possible, giving molecular modelers intuitive control and immediate visual feedback. In this post we’ll walk through how to interactively simulate molecules in SAMSON using force fields and integrators—called interaction models and state updaters in SAMSON’s terminology—and show how these tools help test hypotheses quickly and visually.

Why interactive simulations matter

Suppose you’re trying to understand how a molecule bends, rotates, or resists distortion under specific forces. Rather than launching a long minimization or molecular dynamics run, you can simply pull on the structure and watch how the rest responds. This is not just engaging—it’s a fast way to explore conformational changes or refine structures before performing more detailed simulations.

Setting up your first interactive simulation

To experience this in SAMSON, start by adding a molecule—either from the Asset Browser or by directly placing atoms using the Add editor in the left-side menu. For instance, click anywhere in the viewport to place a single carbon atom.

Next, add a simulator:

Go to Edit > Add simulator or use the shortcut: Ctrl+Shift+M (Windows/Linux) or Cmd+Shift+M (Mac).
Choose Universal Force Field as the interaction model.
Choose Interactive modeling as the state updater.
Optionally name the simulator, then click OK.

Running and controlling simulations

Once the simulator is added, it combines the molecular geometry, the interaction model (force field), and a state updater (integrator). The simulation is now ready to start:

To begin, go to Edit > Start simulation or press X.
To stop, use Edit > Stop simulation or press X again.

At this point, your simulation is live. Try selecting any atom and dragging it slightly. The system responds immediately and continuously adapts, showing how the selected atom perturbs neighboring atoms and the molecular structure. It’s a kinetic form of feedback that bridges the gap between static modeling and dynamic simulation.

Controlling simulation stiffness

If the movements feel too floppy or too stiff, you can tune parameters in the Interactive modeling state updater. Two main variables determine system response:

Step size. A smaller step makes motion smoother and more stable.
Number of steps. Higher values yield a stiffer system with faster forces propagation.

You can adjust both by selecting the state updater and opening the Inspector window.

Takeaways

Interactive simulation in SAMSON is a tactile way to test molecular hypotheses. You can:

See how a molecule responds to perturbations in real time
Quickly detect structural weaknesses or potential conformational states
Avoid launching longer simulations when a quick test suffices

This kind of instant feedback helps reduce modeling time, especially when combined with scripted automation or further energy minimization.

To learn more about simulation and modeling in SAMSON, including details about interaction models and simulators, visit the official documentation: 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.