Molecular modelers spend considerable time optimizing molecular geometries – making sure atoms are in the right place, bonds have the correct length, and everything aligns with physical reality. But clicking through optimization steps and waiting for calculated results can feel disconnected from the intuitive, hands-on experience scientists often prefer. What if there was a way to make geometry optimization feel more tactile and immediate?
SAMSON, the integrative platform for molecular design, offers a distinctive approach to simulation through its interactive modeling feature. With interactive simulations, you can manipulate atoms directly and watch the structure adjust in real time, thanks to integrated force fields and state updaters designed for responsiveness.
What Is Interactive Simulation in SAMSON?
Interactive simulation in SAMSON means you can drag atoms, tweak structures, and instantly observe the system react according to physical models—essentially combining real-time feedback with physical accuracy. This makes building, adjusting, and understanding complex molecular systems much more intuitive.
What You’ll Need
You don’t need a fully prepared molecule to get started. Just add a Carbon atom in the SAMSON viewport from the Add editor panel (also accessible via the Asset Browser). From there, you can apply a simulator and immediately experience real-time structure responsiveness.
Setting Up a Simple Interactive Simulation
- Go to Edit > Add simulator (or press Ctrl + Shift + M on Windows/Linux, Cmd + Shift + M on Mac).
- Choose an interaction model – for example, Universal Force Field (UFF).
- Select a state updater – e.g., Interactive modeling.
- Click OK.
This will set up a dynamic model tied to the chosen force field and updater. You can then start the simulation from Edit > Start simulation (shortcut: X).
Seeing it in Action
Once simulation is running, try dragging an atom. You’ll notice surrounding atoms reconfigure themselves based on the physical model, providing real-time geometry feedback. It’s a valuable teaching tool, as well as a practical method for modeling complex structures, like molecular junctions or nanoscale assemblies.
Interactive modeling also allows parameter adjustments. In the Inspector, you can fine-tune the step size and number of steps to control the system’s responsiveness or stiffness. For example, increasing the number of steps increases resistance to deformation—handy for modeling stiff molecules or minimizing vibration artifacts during dragging.
Why This Matters
This form of hands-on simulation speeds up the iterating process common in molecular modeling. Instead of entering a value, running a calculation and waiting for output, you can simply push an atom and see what happens. It’s especially useful when fine-tuning a geometry just before a full quantum calculation or preparing simulations that depend on precise initial structures.
Tips for Better Results
- Use the Universal Force Field as a flexible default option.
- Start with one or two atoms and gradually build your structure interactively.
- If things “snap” too fast or appear unstable, adjust simulation parameters in the Inspector.
This interactive simulation experience lowers the barrier between modeling intent and simulation results. It facilitates a more natural interaction with molecular systems and removes some of the abstraction often found in computational chemistry tools.
To learn more, check out the official documentation at SAMSON Modeling and Simulation Guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.