When modeling complex molecular systems, geometry optimization is often the first step before moving on to property predictions, docking studies, or simulations. But what if you could optimize your molecules while interacting with them—dragging atoms and watching the structure adapt in real time?
In this post, we’ll explore a lesser-known but powerful feature in SAMSON: interactive geometry optimization using the Universal Force Field (UFF) and state updaters. If you often find yourself looking for a faster and more intuitive way to refine your molecular structures, this could save you time and improve accuracy.
Why optimize interactively?
Many molecular modelers are used to batch geometry optimizations where a molecule is minimized through an algorithm, then returned for analysis. While effective, this approach separates the modeling process from the physical response of the system. SAMSON allows you to run simulations interactively—moving atoms with the mouse while keeping the system physically accurate in real time.
How to set it up
Once you’ve built a molecule (e.g., methane) or added atoms using the Add editor, the interactive geometry optimization workflow only takes a few steps:
- Go to Edit > Add simulator or use Ctrl + Shift + M (Windows/Linux) or Cmd + Shift + M (Mac).
- Choose Universal Force Field (UFF) as the interaction model.
- Select Interactive modeling as the state updater.
- Give the simulator a name (optional) and click OK.
You will see new entries in the Document view for the structural model, dynamical model, interaction model, and simulator:
Start optimizing
Once the simulator is added, you can launch the simulation in one click:
- Edit > Start simulation or simply press X.
Now comes the interactive part: select an atom and drag it. The rest of the molecule will follow in real-time while maintaining physical consistency thanks to the force field.
What’s happening under the hood
Behind the scenes, your simulator coordinates three components:
- Dynamical model – stores degrees of freedom (e.g. atomic positions).
- Interaction model – applies the force field (UFF in this case).
- State updater – integrates motion based on forces (Interactive modeling).
You can fine-tune the behavior of the Interactive modeling state updater by adjusting the number of steps and step size. Increasing the number of steps makes the system stiffer—useful for refining specific geometries or ensuring numerical stability during drag operations.
When to use it
This interactive approach is especially helpful when:
- You need to quickly estimate how a molecule responds to strain or displacement.
- You’re creating representative geometries for animations or educational visuals.
- You want to adjust small structural features before running full-scale simulations.
Final thoughts
Interactive geometry optimization in SAMSON helps bridge physical accuracy and usability, giving you more control over your molecular modeling workflow. It’s a practical approach to improving molecular geometries in real time with visual and physical feedback.
To learn more about modeling and simulation features in SAMSON, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.