htmd.membranebuilder.globalminimization module

htmd.membranebuilder.globalminimization.minimize(lipids: list, box: list | ndarray, stepxy: float = 0.5, steprot: float = 50, contactthresh: float = 2.6) → tuple

Minimize lipid packing by reducing inter-lipid contacts via basin-hopping.

Jointly optimizes the XY positions and Z-rotation angles of all lipids in a single leaflet using SciPy’s basin-hopping algorithm on an L-BFGS-B inner minimizer. The objective function counts the number of inter-lipid atom contacts within contactthresh Angstroms.

Parameters:

• lipids (list) – List of _Lipid objects with mol, xyz, headname, and neighbours attributes.

• box (list or np.ndarray) – Periodic box dimensions used for minimum-image wrapping of inter-lipid distances.

• stepxy (float) – Maximum XY displacement (Angstroms) per basin-hopping step.

• steprot (float) – Maximum rotation displacement (degrees) per basin-hopping step.

• contactthresh (float) – Distance threshold in Angstroms below which two atoms are counted as in contact.

Returns:

• newpos (np.ndarray) – Optimized XY positions for each lipid, shape (N, 2).

• newrot (np.ndarray) – Optimized Z-rotation angles in degrees, shape (N,).