When you adjust a molecular structure by hand, it can be difficult to tell whether the geometry is responding coherently—or to get back to the arrangement you started with. Interactive simulation offers a way to manipulate atoms while a simulator updates the model. Saving a conformation before you begin gives you a useful reference point if you want to revisit the original positions.
Set up a small system
Start with a molecule from SAMSON’s Asset Browser, or use the Add editor to place an atom in the viewport. A small system makes it easier to see how your actions affect the geometry. For the example below, the documentation uses a methane molecule and the Universal Force Field (UFF).
Add the simulator
Choose Edit > Add simulator. The shortcut is Ctrl+Shift+M on Windows and Linux, or Cmd+Shift+M on Mac. In the dialog, choose Universal Force Field as the interaction model and Interactive modeling as the state updater, then press OK.
These names describe different parts of the simulation. The interaction model is the force field: it contains the computed energy and forces. The state updater advances the system’s state. The simulator connects these components to a dynamical model, which contains the system’s degrees of freedom. Knowing which part does what makes the Document view easier to interpret—and helps you locate the relevant settings.
After creating the simulator, you can inspect the UFF interaction model’s properties. To view the Interactive modeling state updater’s properties, select it and open the Inspector. Its step size and number of steps can be modified; the documentation notes that increasing the number of simulation steps can increase system stiffness.
Manipulate while the simulation runs
Start the simulation with Edit > Start simulation or press X. Select an atom in the methane molecule and drag it slowly. The rest of the molecule should follow as the interactive simulation responds. This is useful when you want to explore a geometry through direct manipulation rather than making a change and only inspecting the result afterward.
To pause the process, choose Edit > Stop simulation or press X again. The simulator, its interaction model, state updater, and associated dynamical model are added to the Document view. Think of this view as a record of the pieces involved, not just a list of atoms: the structural model holds atoms and bonds, while the dynamical and interaction models support the simulation.
Keep a before-and-after state
Before experimenting, select the structural model or group of atoms whose positions you want to preserve, then choose Edit > Conformation or press S. A conformation stores the positions of that structural model or atom group—like a single frame in a trajectory. You can restore it by double-clicking its node in the Document view, or by right-clicking and choosing Restore conformation.
This simple habit separates exploration from commitment: you can try a manipulation, compare the resulting geometry with the saved state, and restore the earlier positions when needed. If you save several 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. Conformations are also saved when you save the document as a .sam or .samx file.
A useful way to think about the workflow
Use interactive simulation to explore how a structure responds to your manipulation; use conformations to preserve specific positions and make them recoverable. They solve different parts of the same practical problem: interacting with a model without losing track of the states you may want to compare. For more details, see the SAMSON Modeling and Simulation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.