Getting Your First Molecular Simulation Running in SAMSON

Getting started with molecular modeling can be overwhelming—especially when it comes to setting up interactive simulations. A recurring challenge for researchers, educators, and students alike is simply launching their first simulation to see how their molecule moves, reacts, or relaxes in a virtual environment.

If you’ve ever found yourself wondering how to go from a static model to a physically responsive simulation, this guide shows how to take that first important step in SAMSON, the integrative platform for molecular design.

Why Interactive Simulation Matters

In SAMSON, simulation is not a black box that runs in the background. Instead, it’s interactive—you can manipulate atoms in real time, observe how the geometry adapts, and get immediate feedback on molecular behavior. This is great for educational demos, fast prototyping, and intuitive design of molecular systems.

A Simple Workflow: Add & Simulate

Let’s walk through how to apply a simulator to see how a molecule responds during an interactive simulation:

  1. Add a Molecule: You can either add a predefined molecule using the Asset Browser, or quickly drop an atom into the viewport using the Add editor (add editor). By default, this will add a Carbon atom.
  2. Insert a Simulator: Use Edit > Add simulator or press Ctrl+Shift+M on Windows/Linux (Cmd on Mac).
  3. Select Simulation Components:
    • Interaction model: Universal Force Field.
    • State updater: Interactive modeling.
  4. Launch the Simulation: Click Edit > Start simulation or press X.

Add simulator

Visual Feedback and Control

After setup, SAMSON automatically links the simulator to the relevant data nodes (dynamical model, force field, etc.). Here’s what you should see in the Document view:

  • The structural model (atoms and bonds).
  • A particle system representing degrees of freedom.
  • The Universal Force Field (UFF) interaction model.
  • Interactive modeling as the state updater.

Simulator in the document view

Try It—Drag an Atom

Select an atom in your molecule and drag it gently. You’ll notice how the geometry adjusts based on physical constraints. This interactive behavior makes it easier to explore hypotheses and gain intuition about molecular flexibility.

Interactive simulation with UFF and interactive modeling state updater

Tweak and Explore

Want to fine-tune things? The Interactive modeling updater lets you change properties like step size and number of steps. Increasing the number of steps can make the simulation feel stiffer—providing more resistance to deformation as atoms are dragged.

Hovering between research, exploration, and learning, this approachable simulation setup in SAMSON strikes a nice balance between speed and physical relevance. It’s an easy way to add motion—and meaning—to your molecular models.

To learn more or explore advanced examples, visit the official documentation page on 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.

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