Dragging an atom and watching the rest of a molecule respond can make a modeling session feel intuitive—but only if the simulation is configured correctly. Otherwise, it may be unclear which component controls the forces, how the geometry is being updated, or how to preserve a useful structure before experimenting.
In SAMSON, interactive simulation brings those pieces together: an interaction model calculates forces, a state updater advances the system, and a simulator coordinates them with a dynamical model. That distinction is useful when troubleshooting. The force field and the updater have different jobs, even though both are part of the same simulation.
Start with a small, inspectable system
For a first test, add a molecule from the Asset Browser, or use the Add editor to place an atom in the viewport. A small system makes it easier to see what changes when you manipulate the structure. If you are new to creating molecular systems, see the Building molecules guide.
Next, choose Edit > Add simulator. The shortcut is Ctrl+Shift+M on Windows and Linux, or Cmd+Shift+M on Mac. Select Universal Force Field as the interaction model and Interactive modeling as the state updater, then press OK. You can give the simulator a name if that helps you recognize it later.
The Universal Force Field supplies the interaction model in this example; Interactive modeling supplies the state updater. SAMSON creates an associated dynamical model as part of the simulator setup. In the Document view, these related nodes are visible alongside the structural model, which contains the atoms and bonds. Seeing that organization helps answer a common question: the simulator is not the molecule itself, but a set of components applied to its dynamical model.
Run the simulation, then interact gently
Start the simulation with Edit > Start simulation or press X. To stop it, use Edit > Stop simulation or press X again. With a molecule such as methane, select an atom and drag it slowly. The other atoms should respond as the simulation runs, giving you a direct view of how the system changes under manipulation.
If the behavior is not what you expect, inspect the components rather than treating the simulator as a single black box. Select the Interactive modeling state updater and open it in the Inspector to view its properties. The step size and number of steps can be modified. The documentation notes that increasing the number of simulation steps can increase the stiffness of the system; adjust these settings deliberately and observe the effect rather than changing several things at once.
Keep useful structures before continuing
Interactive exploration can leave you with a geometry you want to revisit. Before making further changes, select the structural model or a group of atoms and choose Edit > Conformation, or press S. This stores the selected atoms’ positions as a conformation. Restore it later by double-clicking its node in the Document view, or by right-clicking and choosing Restore conformation.
Conformations can also be combined into a path when they contain the same set of atoms. Select the conformations, right-click, and choose Conformation > Create path from conformations. The resulting path can be explored with Path Analyzer. Saving the document as a .sam or .samx file also saves its conformations.
The practical takeaway: identify the force model and state updater, start with a manageable structure, manipulate atoms gradually, and save positions you may want to compare. 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.