A molecular model can look perfectly manageable until you move an atom, cut a structure, or join two components. Suddenly, bonds and angles are distorted, and it is hard to tell whether the geometry will settle into a reasonable arrangement. In SAMSON, interactive simulation lets you manipulate a structure while a simulator updates it; for a quick geometry relaxation, the documentation also demonstrates the FIRE state updater.
The useful distinction is that these workflows serve different purposes. Interactive modeling is handy when you want to guide atoms by hand and watch the surrounding structure respond. Geometry optimization is useful when you want a structure to relax after a change. In both cases, the simulator combines a dynamical model, an interaction model (the force field), and a state updater (the integration or update method).
Set up an interactive simulator
Start with a molecule from SAMSON’s Asset Browser, or add an atom using the Add editor. Then choose Edit > Add simulator (Ctrl+Shift+M on Windows and Linux; Cmd+Shift+M on Mac). For the example workflow, select Universal Force Field as the interaction model and Interactive modeling as the state updater. Give the simulator a name if useful, then press OK.
To begin, choose Edit > Start simulation, or press X. While it is running, select and slowly drag an atom. In the documented methane example, the molecule follows the dragged atom as the simulation responds. Press X again, or choose Edit > Stop simulation, when you want to pause.
Adjust the response instead of forcing the structure
If the structure feels too soft or does not respond as you expect, inspect the Interactive modeling state updater’s properties. The documentation identifies two settings you can modify: step size and number of steps. It notes that increasing the number of simulation steps can increase system stiffness. Rather than making large edits all at once, try changing these settings and moving an atom slowly so you can observe how the structure responds.
The Document view helps make the setup less opaque. A simulator is represented alongside the structural model, particle system, interaction model, and state updater. The structural model holds the atoms and bonds; the particle system is the dynamical model containing the system’s degrees of freedom; and the interaction model contains the computed energy and forces. Seeing these pieces together can help when checking which model and updater are associated with a simulation.
Use relaxation after a structural edit
For a geometry-optimization example, the documentation shows a carbon nanotube being sliced and then quickly relaxing toward a mostly flat graphene sheet using the FIRE state updater. This illustrates a useful pattern: make a structural change, then let an optimization workflow relax the resulting geometry rather than treating the edited coordinates as the finished structure.
Interactive modeling and geometry optimization are not interchangeable. Use interactive simulation when you want to steer the model and observe its response as you work. Use a suitable optimization workflow when the goal is to relax a modified geometry. The examples here are starting points, not a guarantee that every structure or force field is appropriate for every scientific question.
Keep a recoverable starting point
Before experimenting, save the current coordinates as a conformation: select the structural model or atom group and choose Edit > Conformation (shortcut: S). To return to that state, double-click the conformation in the Document view, or right-click it and choose Restore conformation. This gives you a simple way to preserve a reference state while trying changes.
If you save several conformations for the same atoms, you can select them and use Conformation > Create path from conformations to make a trajectory, then explore it with Path Analyzer. Conformations are also saved when the document is saved as a .sam or .samx file.
For the full workflow and related concepts, see the SAMSON Modeling and Simulation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.