Interactive simulation can be a game-changer when modeling molecules. Instead of building a molecular structure, launching a long simulation, and then checking the result, what if you could poke, prod, and drag atoms—and see in real time how the molecule reacts and adapts? That’s exactly what interactive simulation in SAMSON enables.
This blog post walks you through the essential steps of performing interactive simulations using the Universal Force Field (UFF) and the Interactive modeling state updater. If you’ve ever wished for instant visual feedback on your molecular designs, this is for you.
Why interactive simulation matters
When tuning a structure or testing a hypothesis in early stages of molecular design, running lengthy simulations might be overkill. Interactive simulations allow you to get a sense of the dynamic response of a system—while you directly manipulate atoms in the viewport.
This can be particularly helpful for:
- Quick stress-testing of conformations
- Educational demos to show chemical behavior
- Identifying regions of steric clash or tension
Setting up an interactive simulator
Start by creating or importing a molecule in SAMSON. If you don’t already have a model, it’s easy to generate one by selecting the Add editor and clicking in the viewport to place atoms.
Then add a simulator:
- Click Edit > Add simulator or use the shortcut Ctrl+Shift+M (on Windows/Linux) or Cmd+Shift+M (on Mac).
- Select the Universal Force Field as the interaction model.
- Choose Interactive modeling as the state updater.
Once added, the simulator groups together the force field (interaction model), degrees of freedom (dynamical model), and the integration algorithm (state updater). These components work together to simulate molecular behavior.
Starting the simulation
To begin or stop the simulation, simply:
- Edit > Start simulation or press X.
- To stop it, use the same steps.
As the simulation runs, SAMSON dynamically updates atom positions in response to interactions, forces, and your direct manipulations.
Try it: drag and observe
Select an atom—say, in a methane molecule—and drag it gently. You’ll notice how the neighboring atoms and bonds respond in real time, striving to maintain minimized energy as governed by UFF:
Tune for responsiveness
You can adjust how the simulation responds by modifying parameters of the state updater via the Inspector. Changing the step size and number of simulation steps lets you control system stiffness—larger values make the molecule resist deformation more strongly.
Benefits and limitations
Interactive modeling isn’t a replacement for rigorous analysis, but it’s an excellent first-pass filter and design tool. Visual feedback is immediate, intuitive, and useful when screening conformations or building structural intuition.
To learn more, read the full documentation on Modeling and Simulation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.