A molecular scene can look like one thing while containing several different kinds of information. A protein’s geometry, the way it is drawn, its possible motion, and the forces acting on it are related—but they are not the same. When you are trying to understand or edit a document in SAMSON, mixing these roles can make a simple task confusing: are you changing the structure, its appearance, or how it behaves in a simulation?
A useful way to sort things out is to ask five questions. Each points to a different model category.
1. What is the system’s geometry and topology?
If the information describes atoms, bonds, or higher levels of organization such as molecules, chains, and residues, you are looking at the structural model. It describes what the nanosystem is made of and how its parts are organized. Think of it as the answer to: “What is here, and how is it connected?”
2. How is the system being drawn?
A visual model provides a graphical representation of structural information. A protein’s secondary-structure view, a Gaussian surface, an electron-density isosurface, or a volumetric electrostatic-field representation are examples. Changing a visual model changes how information is presented; it does not, by itself, mean the underlying molecular structure has changed.
SAMSON supplies visual models by default, and more can be added through SAMSON Connect or provided by Extensions. To apply one, select the relevant nodes—or leave nothing selected to apply it to the whole document—and use the selection’s context toolbar, Visualization > Add > Visual model, or Ctrl/Cmd + Shift + V.
Some visual models expose parameters in the Inspector. Select the visual model in the Document view and choose Inspect from its context menu to view those parameters. This is especially useful when you want to adjust a representation rather than edit the molecular structure.
3. Where can the system move?
A dynamical model indicates the degrees of freedom associated with structural nodes and stores dynamical state information such as positions, momenta, and masses. For example, a particle-system dynamical model applied to atoms assigns three translational degrees of freedom to each atom. Ask: “What parts of this system can change position or state during the calculation?”
4. What energies and forces act on it?
An interaction model describes energies and forces associated with a dynamical model. Examples include Lennard-Jones interactions, spring models, elastic network models, and universal force fields. In the particle-system example, an interaction model can provide the total energy and the force on each particle. This category answers: “What physical or modeled interactions influence the motion?”
5. What information does not fit the first four categories?
A property model represents other properties of a nanosystem. Examples include a scalar such as a protein’s radius of gyration, a scalar or vector field, or a function. If the information is not describing the system’s structure, its graphical representation, its dynamical degrees of freedom, or its energies and forces, it may belong here.
One more distinction: models versus state updaters
State updaters are related to simulation, but they are not one of the five model categories. They implement methods for advancing states, including minimization algorithms, Monte Carlo methods, and molecular dynamics algorithms. A useful mental map is: structural and dynamical models describe the system and its state; interaction models provide energies and forces; a state updater advances the state; visual models help you inspect the result.
When a Document view item is unclear, start with its role rather than its name: does it define the molecular system, show it, describe how it can move, calculate its interactions, or store another property? That small classification step can help you choose the right tool and avoid changing the wrong layer of your model.
For workflows on applying visual models, see Visualizing. For simulation workflows, see Modeling and Simulation. Read the original Models reference to learn more.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.