You open a molecular document and see a clear, polished structure. But when you try to reason about its motion or run a simulation, it is not obvious which parts of the document provide the information needed. The key is that a molecular model’s appearance, structure, dynamics, and forces are different jobs—not interchangeable properties of one object.
SAMSON groups models into five categories. Knowing what each category contributes makes it easier to diagnose a common source of confusion: seeing something in the Document view does not, by itself, tell you what role it plays in a modeling workflow.
Start by asking what the object does
- Structural models: describe geometry and topology. They typically contain atoms and bonds, and can include higher-level nodes such as molecules, chains, and residues. Ask: What is the system made of, and how is it connected?
- Visual models: provide graphical representations, such as a protein’s secondary structure, a surface, an isosurface, or a volumetric field. Ask: How is the system being drawn?
- Dynamical models: indicate the degrees of freedom associated with structural nodes and store dynamical state, including positions, momenta, and masses. For example, a particle-system dynamical model assigns three translational degrees of freedom to each atom. Ask: What can move, and what state describes that motion?
- Interaction models: provide energies and forces corresponding to the degrees of freedom in a dynamical model. Examples include Lennard-Jones, spring, elastic network, and universal force-field models. Ask: What interactions produce the energy and forces?
- Property models: represent properties not covered by the first four categories—for example, a gyration-radius value or a scalar or vector field. Ask: What additional information about the nanosystem is being represented?
Why the distinction matters
A visual model can make a structure easier to interpret, but its purpose is graphical representation. It is not the same thing as the structural model that describes atoms and bonds, or the interaction model that calculates energy and forces. Likewise, an interaction model provides forces for the degrees of freedom described by a dynamical model; it does not replace that dynamical description.
This gives you a practical way to investigate a document: identify what you are looking at, then ask what information your next task needs. If the goal is to inspect molecular organization, focus on the structural nodes. If the goal is to change how the system appears, look for a visual model. If the goal is simulation, consider the dynamical and interaction models together—and remember that a state updater is a separate component used to advance the state.
Keep display and simulation questions separate
When a representation does not look the way you expect, investigate the visual model and its settings. Some visual-model parameters can be inspected by selecting the model in the Document view and choosing Inspect from its context menu. SAMSON also lets you add visual models through the selection’s context toolbar or Visualization > Add > Visual model; with nothing selected, the visual model is applied to the document.
When the question is about motion or forces, a display change is unlikely to answer it. Instead, think in terms of the dynamical model, interaction model, and state updater: respectively, the degrees of freedom and state, the energies and forces, and the method used to advance states during simulation or minimization.
One useful mental shortcut is to trace the roles in order: structure defines the system; dynamics describes its possible state; interactions provide energies and forces; an updater advances the state; visual models help you see it. Property models add other information that does not fit those four roles.
Once these responsibilities are clear, a crowded document becomes easier to interpret. Rather than asking only “What is this object?”, ask “What information does it provide?” That small change can help distinguish a display issue from a missing modeling component.
For details on the model categories and related workflows, see the SAMSON models reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.