molecules

This section maps molecule labels to their topology settings. A molecule can either be created from a template like “star_polymer” or defined as a “custom” structure.

Quantity Specifications

Define how many molecules to instantiate. Note that for any molecule defined under molecules, you must include one of the following count specifications directly within its parameter block:

Option A: Explicit Count

num_molecules: 50

Option B: Ratio to a Reference Molecule

molecule_ratio: 0.5
molecule_ratio_reference: "reference_molecule_name"

Molecule Types & Templates

Specify the structure type using one of the templates or custom structure options below. Each option has its own dedicated page with configuration details, examples, and options:

• Star Polymer
• Linear Polymer
• Ring Polymer
• Comb Polymer
• Grafted Colloid
• Patchy Colloid
• Custom Molecule
• Rigid Body
• Partially Rigid Body