Models#

Use this reference when you need to identify the model categories used in SAMSON documents and understand which category matches the object you see in the Document view.

SAMSON represents nanosystems using five categories of models:

Structural nodes describe geometry and topology.
Visual models provide graphical representations.
Dynamical models describe dynamical degrees of freedom.
Interaction models describe energies and forces.
Property models describe properties that do not enter in the first four model categories.

Apart from these models, SAMSON also has state updaters used in the minimization and simulations.

Models and state updaters are nodes in SAMSON document.

What this reference covers#

This page defines the main model categories in SAMSON. Use Visualizing for the task workflow of adding visual models, and Modeling and Simulation for simulator, interaction model, and state updater workflows.

Structural models#

Structural models describe the geometry and topology of nanosystems in SAMSON. Typically, a structural model contains atoms and bonds, and might contain nodes representing higher organization levels, e.g. molecules, chains, residues, etc.

Visual models#

Visual models are used to provide graphical representations. A visual model may be e.g. a secondary structure representation of a protein, a gaussian surface, an isosurface of an electron density, a volumetric representation of an electrostatic field, etc.

SAMSON provides a set of visual models by default and you can add more from SAMSON Connect (SAMSON Extensions may also provide visual models). You can see some of the default visual models supplied with SAMSON on the image below.

Some default visual models

Visual models are usually applied to selected nodes or to the whole document if nothing is selected as follows:

via the context toolbar menu of the selection
using Visualization > Add > Visual model
shortcut: Ctrl/Cmd + Shift+V

Use Visualizing to learn how to apply visual models.

For some visual models, you can modify their visualization parameters in the Inspector. For that, select the visual model in the Document view and click on Inspect in the context menu.

Secondary structure visual model parameters in the Inspector

The default visual models in SAMSON make it possible to highlight and select atoms, residues, chains, etc. directly via surfaces depending on the current selection filter.

Highlighting residues on the Solvent Excluded Surface

To start developing your own visual models, use the documentation about generating SAMSON Extensions and the Documentation center.

Dynamical models#

Dynamical models are used to indicate where degrees of freedom are in structural nodes. For example, a particle system dynamical model applied to a group of particles (atoms) assigns three translational degrees of freedom to each atom. Dynamical models describe the dynamical state and store positions, momenta, and masses.

Interaction models#

Interaction models are used to represent energies and forces in a dynamical model and are used in SAMSON to perform various modeling and simulation tasks. An interaction model could be, for example, a simple Lennard-Jones model to describe unbounded interactions between a group of particles (atoms), a spring model, an elastic network model, a universal force field, etc.

An interaction model is in charge of providing forces corresponding to the degrees of freedom in a dynamical model. For example, an interaction model applied to a particle system dynamical model provides both the total energy of the particle system and the force applied to each particle (atom) in the particle system.

SAMSON provides a set of interaction models by default and you can add more from SAMSON Connect.

To start developing your own interaction models, use the documentation about generating SAMSON Extensions and the Documentation center.

Property models#

Property models are used to represent properties of nanosystems that are not already described by the first four categories of models. For example, property models may be e.g. a simple number describing the gyration radius of a protein, a scalar field (such as an electron density), a vector field (to represent e.g. an electrostatic field), a function, etc.

State updaters#

State updaters implement methods used to advance states during simulations. State updaters may be e.g. minimization algorithms, Monte Carlo methods, molecular dynamics algorithms, etc.

SAMSON provides a set of state updaters by default and you can add more from SAMSON Connect.

To start developing your own state updaters, use the documentation about generating SAMSON Extensions and the Documentation center.

Node types: understand where models fit in document hierarchy.
Visualizing: add visual models to represent structures.
Modeling and Simulation: use interaction models, dynamical models, and state updaters in simulations.
Extending SAMSON: add or develop model extensions.