A modeling session often involves two competing needs: you want to let a structure move so you can explore its geometry, but you also want to keep track of configurations that may be useful later. In SAMSON, interactive simulation lets you manipulate atoms while a simulator updates the model; conformations let you save and revisit selected structural states. Together, they offer a practical way to explore molecular geometry without treating every change as permanent.
Set up an interactive model
Start with a molecule from the Asset Browser, or use the Add editor to place an atom in the viewport. To create a simulator, choose Edit > Add simulator. On Windows and Linux, the shortcut is Ctrl+Shift+M; on Mac, it is Cmd+Shift+M. For a basic example, select Universal Force Field as the interaction model and Interactive modeling as the state updater, then press OK.
The simulator connects a dynamical model, an interaction model, and a state updater. In SAMSON’s terminology, the force field is an interaction model, while the integrator is a state updater. The dynamical model holds the system’s degrees of freedom; the interaction model contains computed energy and forces; and the simulator coordinates these components.
Start the simulation with Edit > Start simulation or press X. Select an atom and drag it slowly: the molecule should respond as the interactive simulation runs. Press X again, or choose Edit > Stop simulation, to stop. The Interactive modeling state updater also exposes step-size and number-of-steps settings. Adjusting these can change how the system responds; try changing them deliberately and observing the result rather than assuming one setting suits every model.
Save a useful state before you keep exploring
When you reach a configuration you may want to return to, save it as a conformation. Select the structural model or group of atoms, then choose Edit > Conformation or press S. A conformation stores the positions of that structural model or atom group: think of it as one frame, rather than a continuously updating record.
This small habit can make experimentation easier. Save a conformation before making a substantial change, and save another when you reach a configuration worth comparing. You can restore a saved state by double-clicking its conformation node in the Document view, or by right-clicking it and choosing Restore conformation. This gives you a way to revisit a known arrangement instead of relying on memory or trying to recreate it by hand.
Turn saved states into a path
If you have several conformations that store information for the same set of atoms, you can combine them into a path. Select the conformations, right-click the selection, and choose Conformation > Create path from conformations. The resulting path is a trajectory assembled from those saved states, which you can explore further with Path Analyzer.
The key practical distinction is that a conformation records a particular state, while a path organizes a set of compatible conformations into a sequence. Neither replaces careful interpretation of a simulation; they help you preserve and navigate the structures you have chosen to examine.
Keep the work with the document
When you save a SAMSON document as a .sam or .samx file, its conformations are saved as well. That makes saved states useful not only during a session, but also when you return to the document later.
For the full workflow and related modeling concepts, see the SAMSON Modeling and Simulation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.