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htmd.membranebuilder.ljfluid module#

htmd.membranebuilder.ljfluid.distributeLipids(boxsize: list | ~numpy.ndarray, resnames: list, sigmas: ~numpy.ndarray, cutoff: float, mass=39.9 Da, epsilon=0.238 kcal/mol, switch_width=3.4 A, forbidden_xy: ~numpy.ndarray | None = None, forbidden_radii: ~numpy.ndarray | None = None, platform_name: str | None = None) → tuple#

Distribute lipid heads on a 2D plane using a short LJ-fluid simulation.

Lipid heads are modeled as Lennard-Jones spheres whose sigma values are chosen to reproduce the target area-per-lipid in a hexagonally packed monolayer. A Halton-sequence initial placement is followed by an OpenMM Verlet simulation that relaxes the heads into a physical arrangement. Obstacles (e.g. solute footprint atoms) can be provided to exclude lipids from a forbidden XY region.

Parameters:

  • boxsize (list or np.ndarray) – Periodic box dimensions [Lx, Ly, Lz] in Angstroms. The Z extent is used only to define the OpenMM box; lipids are confined to z=0.

  • resnames (list) – Residue names for each lipid particle. Length determines the number of particles.

  • sigmas (np.ndarray) – Per-particle LJ sigma values in Angstroms. Length must match resnames.

  • cutoff (float) – Lennard-Jones cutoff distance in Angstroms.

  • mass (openmm.unit.Quantity, optional) – Particle mass. Defaults to argon mass (39.9 amu).

  • epsilon (openmm.unit.Quantity, optional) – LJ well depth. Defaults to argon epsilon (0.238 kcal/mol).

  • switch_width (openmm.unit.Quantity, optional) – LJ switching function width. Defaults to 3.4 Angstroms (argon).

  • forbidden_xy (np.ndarray, optional) – XY coordinates of obstacle atoms, shape (K, 2). Halton candidates inside any obstacle disk are excluded before the LJ simulation.

  • forbidden_radii (np.ndarray, optional) – Per-obstacle exclusion radii in Angstroms, shape (K,). Required when forbidden_xy is provided.

  • platform_name (str, optional) – OpenMM platform name. If None, OpenMM selects the fastest available platform.

Returns:

  • final_positions (np.ndarray) – Post-LJ-simulation XY head positions for each lipid, shape (N, 3), in the caller’s coordinate frame.

  • initial_positions (np.ndarray) – Pre-simulation Halton-filtered positions, shape (N, 3).

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