If you’ve ever wished you could see how a molecule responds to changes as you make them—like dragging an atom and watching the rest rearrange in real time—then interactive simulation in SAMSON may be exactly what you’re looking for.
One recurring challenge in molecular modeling is the delay between editing a structure and seeing how it physically responds. Traditional workflows often require running simulations as separate steps, making the modeling process slower and more fragmented. This is particularly frustrating during early-stage design or during mechanistic exploration when quick feedback is essential.
Interactive simulation in SAMSON addresses this by letting you manipulate a molecule and watch the simulation adjust in real time. It combines a force field (SAMSON calls this an interaction model), an integrator (or state updater), and real-time feedback inside the modeling environment.
Setting Up an Interactive Simulation
Here’s a step-by-step example for creating a simple interactive simulation using the Universal Force Field (UFF):
- Add any molecule using the Add editor (default atom: Carbon) in the left-side menu.
- To add a simulator, go to Edit > Add simulator (
Ctrl + Shift + Mon Windows/Linux,Cmd + Shift + Mon macOS). - Choose Universal Force Field as the interaction model.
- Select Interactive modeling as the state updater.
- Press OK.
Running the Simulation
- Start the simulation: Edit > Start simulation or press
X. - Stop the simulation: same as above (
X).
Your simulator will now appear in the document view, containing the structural model, the interaction model (UFF), the state updater, and the simulator node that ties them together.
Try It Out: Drag, Watch, Learn
Select an atom—say from a methane molecule—and drag it slowly. The rest of the molecule will respond immediately thanks to the UFF force field and the interactive state updater. This allows you to experiment with geometries, probe flexibility, or test constraints in a highly intuitive way.
Adjust the step size and number of simulation steps to tune the stiffness or responsiveness of the simulation. Smaller steps yield smoother motion, while more steps per frame increase convergence. These settings can be changed from the properties panel of the state updater.
Who Benefits From This?
Interactive simulation is particularly useful for:
- Educators and students visualizing structure-property relationships quickly.
- Researchers testing molecular stability or identifying binding-induced deformations.
- Designers exploring new configurations at very early stages.
By reducing the gap between modeling and simulation, interactive workflows encourage learning through exploration and improve creative throughput.
To learn more, see the official documentation: 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.