For those working in molecular modeling, one common challenge is understanding how computational models translate into actual behavior once simulations are enabled. Did the structural setup contain all necessary parameters? Is the simulation responding as expected when interacting with atoms in real time? Fortunately, SAMSON offers a streamlined way to start interactive simulations and immediately see your molecular systems come alive.
This blog post guides you through setting up and launching a basic interactive simulation inside the SAMSON interface — an important early milestone for anyone beginning with molecular design and chemistry simulations. We’ll look at how to apply a simulator to a simple system, how the models work together, and how to visually verify that everything’s behaving as it should.
What is a Simulator in SAMSON?
A simulator in SAMSON is like an engine that drives the physical evolution of your molecular system. It combines three component models:
- The dynamical model — defines degrees of freedom like atomic positions and velocities.
- The interaction model — computes forces between atoms (e.g., Universal Force Field).
- The state updater — updates the system over time using specific integration methods (e.g., Interactive modeling).
You can add these components through a simple GUI-based workflow inside SAMSON.
Creating a Simple Simulation
To test how simulation affects molecular geometry, you can begin with the most minimal setup — like placing a single atom.
- Switch to the Add editor to place an atom in the viewport. By default, this is a carbon atom.
- Next, to add a simulator, go to Edit > Add simulator.
- In the dialog that opens, select the following:
- Interaction model: Universal Force Field
- State updater: Interactive modeling
- Give your simulator a name if you’d like and click OK.
Once added, SAMSON automatically attaches all components and you’ll see the simulator structure appear in the Document view.
Running Simulations in Real Time
To run your interactive simulation:
- Choose Edit > Start simulation or press X.
You’ll notice something immediate — you can now drag atoms in the viewport, and the entire system will respond in real time thanks to the applied force fields and dynamics. This helps visualize potential energy surfaces, structural relaxation, and more — without having to wait for batch simulations.
Adjusting Dynamics
Need a stiffer or softer system response? You can tweak:
- Step size — defines how much the atomic positions can change per iteration.
- Number of steps — more steps per update increases overall responsiveness.
These settings can be accessed via the Inspector once you select the state updater.
Why It Matters
Real-time visual feedback significantly reduces turnaround time for validating whether a setup “works” before committing to longer calculations. Especially useful in educational settings, quick geometry tweaks, or when exploring new systems, SAMSON’s interactive approach makes simulation more tangible and understandable.
This also provides a great environment for iterative workflows — you modify atom positions, rerun the interactive engine, and observe the energy-driven adjustments immediately.
Ready to dive deeper or apply these principles to more complex systems? Explore the full documentation on SAMSON’s simulation capabilities here: 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.