When working on molecular modeling, seeing immediate feedback from your simulation can make all the difference. Whether you’re adjusting geometries or exploring structural responses, waiting for batch simulations can slow down discovery and reduce intuition. This is where interactive simulation in SAMSON becomes useful for fast prototyping and learning.
SAMSON supports simulations that run in real time, meaning you can exert forces on molecules—like grabbing and moving an atom—and instantly observe how the rest of the molecule reacts based on physical models. This interactive experience creates a more natural way to understand and explore molecular behavior.
Simulation in Motion
Interactive simulations in SAMSON rely on three key components:
- Interaction model: Describes how atoms interact, typically a force field such as the Universal Force Field (UFF).
- State updater: Defines how the system moves or evolves over time; for interactive simulations, this is often the “Interactive modeling” updater.
- Dynamical model: Stores the degrees of freedom of your system, enabling motion.
These are all linked through a simulator node you can add in the document view. The result is a system that responds live to user interactions.
Trying It Yourself
To set this up in SAMSON:
- Either add a molecule from the Asset Browser or add an atom manually using the Add editor.
- Go to Edit > Add simulator or press Ctrl+Shift+M (Cmd on Mac).
- Select the Universal Force Field as the interaction model.
- Choose Interactive modeling as the state updater.
- Name the simulator (optional) and press OK.
You should now see corresponding nodes in the Document view for the dynamical model, interaction model, and simulator. Start the simulation by clicking Edit > Start simulation or pressing X.
Live Molecular Manipulation
Select an atom—say, in a methane molecule—and gently drag it using your mouse. The interactive simulation will calculate the forces and the other atoms will follow the motion realistically, honoring the constraints of the applied force field.
This interactive feedback loop is powered by the step size and number of simulation steps you configure in the state updater. Increasing the number of steps can make the molecule feel more rigid or stable as you interact with it, while a higher step size may make the system respond more quickly—but potentially less accurately.
For prototyping molecules or educational settings, this mode offers a uniquely hands-on experience. It can help you grasp molecular mechanics with immediate visual feedback—no need to wait for a simulation to render after every small adjustment.
When to Use It
Interactive simulations can be helpful when:
- You want to quickly test how structural changes affect geometry and forces.
- You aim to build molecules intuitively by pulling and adjusting elements.
- You’re teaching concepts of molecular mechanics and need immediate demos.
They aren’t designed for detailed force field exploration or long timescale dynamics, but they provide an efficient way to iterate and understand systems in early design stages.
To learn more about simulators in SAMSON, visit the full documentation page: Modeling and Simulation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.