Custom Molecule

For molecular structures not covered by standard polymer or colloid templates, you can define them explicitly as a "custom" structure using Cartesian coordinates and bonded connectivity groups.

Overview

Custom structures allow explicit specification of:

• particle_positions: List of Cartesian coordinates [x, y, z] for each constituent particle.

• particle_typeid: Integer particle type ID assigned to each particle.

• bond_groups & bond_typeid: Pairs of particle indices forming bonds and their corresponding bond type IDs.

• angle_groups & angle_typeid (optional): Triplets of particle indices forming angles and their type IDs.

• dihedral_groups & dihedral_typeid (optional): Quartets of particle indices forming dihedrals and their type IDs.

YAML Configuration Example

The following example defines a 4-bead linear tetramer with bonds, angles, and a dihedral:

molecule_type: "custom"
num_molecules: 10
particle_positions:
  - [0.0, 0.0, 0.0]
  - [0.0, 0.0, 1.0]
  - [0.866, 0.0, 1.5]
  - [0.866, 0.5, 2.366]
particle_typeid: [0, 1, 1, 2]
bond_groups:
  - [0, 1]
  - [1, 2]
  - [2, 3]
bond_typeid: [0, 0, 0]
angle_groups:
  - [0, 1, 2]
  - [1, 2, 3]
angle_typeid: [0, 0]
dihedral_groups:
  - [0, 1, 2, 3]
dihedral_typeid: [0]