A small change to a molecular structure can leave atoms in awkward positions. The challenge is not only to see that the geometry looks wrong, but to let the system respond to your edits while you work. In SAMSON, an interactive simulation can help: you drag an atom, and the molecule responds under a force field rather than remaining a static drawing.
This walkthrough uses a simple methane molecule to show how to set up that workflow, what its components mean, and how to keep useful structural states as you experiment.
Set up a small test system
Start with a molecule from the Asset Browser, or build a simple system in the viewport. For a first test, methane is useful because it is small enough to inspect while you learn the controls. Before adding a simulator, make sure the molecule is selected or visible in the document so you can easily identify its structural and simulation components afterward.
Choose Edit > Add simulator. The documented example uses the Universal Force Field as its interaction model and Interactive modeling as its state updater. These names describe different jobs: the interaction model is the force field, while the state updater advances the model’s state. The simulator connects these pieces to the dynamical model, which holds the system’s degrees of freedom.
After choosing the models, press OK. You can inspect the interaction model’s properties in its property window. To view the state updater’s properties, select it and open the Inspector. This distinction is useful when you are adjusting a simulation: force-field settings and the way the state is updated belong to different components.
Start, interact, and tune
Start the simulation from Edit > Start simulation, or press X. The same shortcut is listed for stopping it, so use the menu command if you want an explicit start or stop action. Once the simulation is running, select an atom in methane and drag it slowly. The molecule should follow the movement of the atom as the simulation updates its geometry.
If the response feels too soft or too stiff for your test, inspect the Interactive modeling state updater. Its step size and number of steps can be modified; the documentation notes that increasing the number of simulation steps can increase the system’s stiffness. Change these settings deliberately, one at a time, and observe the effect. That makes it easier to understand which setting changed the response instead of treating the simulator as a black box.
Think of the Document view as a useful map of the setup. The structural model contains atoms and bonds; the particle system is the dynamical model; the interaction model contains the computed energy and forces; and the simulator refers to these pieces along with its state updater. If you later need to understand what is being simulated, inspecting this tree is more informative than looking at the molecule alone.
Keep a before-and-after state
Interactive work is exploratory, so preserve states you may want to revisit. Select the structural model or the relevant group of atoms, then choose Edit > Conformation or press S. A conformation stores the positions of that structure, much like one frame in a trajectory. Restore it later by double-clicking its node in the Document view, or by right-clicking and choosing Restore conformation.
When you have multiple conformations for the same set of atoms, select them and choose Conformation > Create path from conformations from the context menu. The resulting path can be explored with Path Analyzer. Saving the document as a .sam or .samx file also saves its conformations, so your recorded states remain part of the project.
The key practical idea is to separate editing from recording: use interactive simulation to explore how a structure responds, then save conformations at states worth comparing. For a different task—quick geometry optimization—the documentation also demonstrates the FIRE state updater, including an example where a sliced carbon nanotube relaxes toward a mostly flat graphene sheet. Choose the workflow that matches the question you are asking, rather than expecting one setup to serve every modeling goal.
For the complete walkthrough and related references, see the SAMSON Modeling and Simulation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.