Units and Conventions

Faunus inputs use explicit physical units where a field requires them. Unless a field or YAML tag states otherwise, use the conventions below.

Quantity	Unit or convention	Common fields
Length	Å	Cell dimensions, positions, cutoffs, sigma, bond lengths, histogram bins
Energy	kJ/mol	Pair potentials, bonded terms, tabulated potentials, energy output
Temperature	K	system.medium.temperature
Charge	Elementary charge, e	Atom charge values and electrostatic analyses
Mass	g/mol	Atom mass values and PSF output
Activity or concentration	mol/L	Atom and molecule activity, salt concentrations, molarity collective variables
Pressure	Tagged units	!atm, !bar, !Pa, !kT, and !mM in system.energy.pressure
Topology angles	Degrees	Torsion and dihedral equilibrium angles such as aeq and phi
Move angles	Radians	Angular MC move sizes such as !RotateMolecule {max_angle: ...}

Input conventions

YAML tags select physical models, units, and constructors. Examples include !Water for the dielectric model, !NaCl for salt, !Cuboid for a cell, and !atm for pressure.

In a complete simulation input, energy terms belong under system.energy. Included force-field fragments may use a top-level energy section that is merged into the complete input.

Selection expressions are strings, for example "molecule protein and name CA". They use the selection language described in Selection Language.

Use YAML comments (#) for lines or blocks. Faunus also ignores top-level keys whose name starts with _, which is useful for temporarily disabling whole sections while keeping the input valid YAML. Template inputs can also use MiniJinja block comments; see Comments.

Names

Atom type names come from the top-level atoms list and are used by force-field parameters and atomtype selections. Per-atom names come from molecule definitions, structure files, or atom_names, and are used by name selections.

Molecule names identify molecule types in molecules, system.blocks, moves, and analyses. In selection strings, quote names that contain spaces or collide with selection keywords.

Output conventions

The main output.yaml file reports the final simulation summary, energy terms, move statistics, and analysis summaries. Analyses with a file: field write their own data files. Column headers include units where possible, for example z/Å, W/kJ/mol, or molarity/mol·L⁻¹.