Rigid Body¶

Setting rigid: true treats the entire custom molecule as a single HOOMD-blue rigid body where all constituent particles remain fixed relative to a central reference bead.

Overview¶

In HOOMD-blue, rigid bodies consist of a central particle that carries the body’s center-of-mass translation and rotation, plus constituent particles whose relative positions and orientations are locked with respect to the center:

Central Reference Bead (Index 0): The first particle in particle_positions defines the center and orientation of the rigid body.
Constituent Beads (Indices 1 to N): All subsequent particles in particle_positions are registered as constituent particles fixed to the central particle.
Integration: When setting up the simulation integrator, use a Rigid filter (e.g. with flags: ["center", "free"]) so that HOOMD integrates the central particle while freezing relative motion of constituent particles.

YAML Configuration Example¶

The following example configures a 12-bead monoclonal antibody (mAb) with a flexible hinge dimer, Fc stem, and two Fab arms as a wholly rigid structure:

molecule_type: "custom"
rigid: true
num_molecules: 5
particle_positions:
  - [0.0, -0.2, 0.0]    # Bead 0: Hinge dimer (central reference point)
  - [0.0, 0.2, 0.0]     # Bead 1: Hinge dimer
  - [0.0, 0.0, -1.0]    # Bead 2: Fc stem (blue)
  - [0.0, 0.0, -2.0]    # Bead 3: Fc stem tip (red)
  - [-0.866, 0.0, 0.5]  # Bead 4: Left Fab arm base (1-2-1 segment 1)
  - [-1.732, -0.5, 1.0] # Bead 5: Left Fab arm split A (1-2-1 segment 2)
  - [-1.732, 0.5, 1.0]  # Bead 6: Left Fab arm split B (1-2-1 segment 2)
  - [-2.598, 0.0, 1.5]  # Bead 7: Left Fab arm tip (1-2-1 segment 3)
  - [0.866, 0.0, 0.5]   # Bead 8: Right Fab arm base (1-2-1 segment 1)
  - [1.732, -0.5, 1.0]  # Bead 9: Right Fab arm split A (1-2-1 segment 2)
  - [1.732, 0.5, 1.0]   # Bead 10: Right Fab arm split B (1-2-1 segment 2)
  - [2.598, 0.0, 1.5]   # Bead 11: Right Fab arm tip (1-2-1 segment 3)
particle_typeid: [0, 0, 1, 2, 1, 1, 2, 2, 1, 1, 2, 2]