Moving an atom by hand can be a quick way to explore a molecular structure—but it can also leave you wondering whether the rest of the molecule will respond sensibly. Interactive modeling offers a way to manipulate atoms while a simulator updates the system, so you can observe the geometry change as you work.
This workflow is useful for hands-on exploration, not a substitute for checking whether a chosen model is appropriate for your scientific question. The example below uses SAMSON’s Universal Force Field (UFF) interaction model and Interactive modeling state updater to make a small system respond as an atom is dragged.
What is running when you start a simulation?
In SAMSON, a simulator connects three pieces: a dynamical model, which represents the system’s degrees of freedom; an interaction model, which calculates energies and forces; and a state updater, which updates the system’s state. In this example, UFF is the interaction model and Interactive modeling is the state updater.
This distinction helps when setting up or troubleshooting a simulation. A force field and an integrator may be familiar terms in other software; SAMSON calls these components interaction models and state updaters. The simulator keeps the components associated, and the interactive workflow lets you continue acting on atoms while it runs.
A small, repeatable setup
- Add a molecule from the Asset Browser, or use the Add editor to place an atom in the viewport. The documentation’s example uses a methane molecule.
- 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.
- Start the simulation with Edit > Start simulation, or press X. Press X again to stop it.
Once it is running, select an atom in the methane molecule and drag it slowly. The other parts of the molecule should respond, letting you see the interactive modeling behavior rather than only the result of a static edit.
If the response feels too soft or too stiff
The Interactive modeling state updater exposes settings for step size and number of steps. These are practical controls to inspect if the system’s response does not feel suitable for the task. The documentation notes that increasing the number of simulation steps can increase system stiffness. Rather than changing several settings at once, adjust one parameter, repeat the same slow drag, and compare the response. This makes it easier to understand what changed.
Keep the goal of the session in mind: interactive response is useful for geometry exploration, but the fact that a structure moves smoothly does not by itself establish that a model or result is appropriate for a particular scientific use. For details about the UFF implementation in SAMSON, consult the cited paper linked from the documentation.
Keep useful states instead of relying on memory
When you reach a geometry worth revisiting, select the structural model or the relevant group of atoms and choose Edit > Conformation, or press S. A conformation stores the positions of that structural model or atom group, like a single frame. You can restore it by double-clicking its node in the Document view, or by right-clicking and choosing Restore conformation.
If you have 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. This gives you a simple way to preserve and review alternative states instead of trying to recreate a promising arrangement from scratch. Conformations are also saved when the document is saved as a .sam or .samx file.
The complete Modeling and Simulation guide covers simulator setup, examples, conformations, and related workflows.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.