One of the surprisingly frustrating moments in molecular modeling comes when you’re trying to intuitively edit a geometry — say, nudge an atom — and your software either resists or breaks the whole system. Traditional modeling tools often require repeated cycles of dragging, optimizing, and restarting. But what if you could combine direct manipulation and simulation, in real-time?
That’s exactly what SAMSON enables with its interactive simulation system. In this post, we’ll walk through a key capability: launching an interactive simulation that responds in real time to user actions such as dragging atoms. If you’re working with molecular systems and need to understand geometry flexibility on the fly, this feature could save you time and help avoid overcorrections.
Direct Simulation Feedback While Editing
SAMSON supports simulations that update dynamically as you edit geometry. This means that when you grab an atom and move it, the molecular system responds with physically meaningful deformations — rather than just stretching bonds or breaking things.
This is made possible by the way simulators are defined in SAMSON. Each simulator groups together:
- a dynamical model representing degrees of freedom
- an interaction model (i.e., a force field like UFF)
- a state updater, which acts like an integrator (e.g., Interactive modeling)
When you start a simulation, SAMSON brings these models together and continuously applies the force field and updates atomic positions in response to your interactions.
How to Try It Yourself
To run a basic interactive simulation:
- Add a molecule via the Asset Browser or insert an atom using the Add editor.
- Go to Edit > Add simulator or use the shortcut
Ctrl+Shift+M(orCmd+Shift+Mon Mac). - Select the Universal Force Field (UFF) as the interaction model.
- Choose Interactive modeling as the state updater.
- Optionally name your simulator and click OK.
You will see the simulator added to your Document view. To start the simulation, use:
- Edit > Start simulation or the
Xshortcut key
You can stop the simulation with the same shortcut or by selecting Edit > Stop simulation.
What to Expect
Once the simulator is running, try dragging an atom from a molecule like methane. You’ll start to see the rest of the molecule respond — bonds stretch realistically, forces are updated instantly, and the system tries to preserve its integrity based on the UFF potential.
This capability gives you a better understanding of molecular flexibility and strain without needing to manually request and wait for an optimization after every adjustment.
Customize Simulation Parameters
You can adjust the stiffness of the simulation by selecting the state updater in the Document view and modifying its properties in the Inspector. Two key parameters are:
- Step size – controls how far the atoms move per update
- Number of steps – affects the computation depth at each interaction
Tune these live to find the sweet spot between responsiveness and simulation realism. The simulation can feel either fluid or strongly constrained depending on these settings.
To learn more about simulations in SAMSON, visit the full documentation at https://documentation.samson-connect.net/users/latest/modeling-and-simulation/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.