Simulating molecular movement is a core task for many researchers, but getting immediate feedback from changes made in a visual editor is often time-consuming or unavailable altogether in some tools. One common pain point in molecular modeling is not being able to interact with your model while seeing the physical effects of your changes in real-time — especially when doing initial geometry relaxation or testing hypothesis about molecule behavior under structural changes.
Enter interactive simulation in SAMSON: a flexible feature that allows users to make real-time changes to atomic positions and immediately see how the simulated system responds. You can grab atoms, pull them, and the force field responds right away to your inputs. It bridges the gap between modeling and simulation in a highly intuitive visual environment.
How Interactive Simulation Works
At the core of SAMSON’s interactive simulation are three components:
- Interaction model – this is essentially the force field, such as the Universal Force Field (UFF), that computes energies and forces.
- State updater – this works as an integrator that determines how atoms move according to the forces (e.g., Interactive modeling).
- Dynamical model – this contains the degrees of freedom (how the atoms can move) of the system.
Once you set up a simulation system with these components, you can start and stop the simulation using a simple keyboard shortcut or through the Edit menu. While the simulation is running, any movement to atoms (e.g., dragging with the mouse) immediately causes a response due to the interaction model’s recalculated forces.
Setting Up an Interactive Simulation
Here’s a quick overview of how to get started with an interactive simulation in SAMSON:
- Add an atom using the Add Editor in the left-side menu — by default, it will be Carbon.
- Open the simulator creation dialog: Edit > Add simulator or via CtrlShiftM (Windows/Linux) or CmdShiftM (Mac).
- Select the Universal Force Field as your interaction model.
- Select Interactive modeling as your state updater.
- Press OK.
You’ll see the newly created simulator show up in the Document view, with links to each sub-model. Each model is independently inspectable, and their properties — such as step size or number of steps — can be edited in the Inspector.
Visual & Intuitive Modeling
Once everything is configured, hit X to start the simulation. Now click and drag any atom. You’ll immediately see the molecular system try to follow the dragged atom, responding as if under an actual physical constraint.
This feature makes it easy to refine molecular geometries, test how structural deformations affect a molecule, or simply learn how molecules behave. You can also adjust parameters to make the system behave more softly or stiffly, depending on your modeling needs.
Why This Matters
Instead of following a build-then-test simulation workflow, SAMSON’s interactive simulation lets you combine them. This is particularly useful in early-stage model validation, educational environments, or whenever you need visual and tactile feedback from molecular systems. It lowers the barrier to entry for simulation, making it feel more like sculpting than coding.
If you want to explore further, such as using reactive force fields or more advanced state updaters, check out the full documentation at SAMSON’s Modeling and Simulation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.