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htmd.membranebuilder.build_membrane module#

htmd.membranebuilder.build_membrane.buildMembrane(xysize, ratioupper, ratiolower, waterbuff=20, platform='CUDA', minimize=0, equilibrate=0, outdir=None, lipidf=None, forcefield_files=None, seed=None, solute=None, timestep_fs=2.0, head_z=15.0, head_restraint_k=0.0)#

Construct a membrane containing arbitrary lipids and ratios of them.

Parameters:

  • xysize (list) – A list containing the size in x and y dimensions of the membrane in Angstroms

  • ratioupper (dict) – A dict with keys the molecule names and the ratio of that molecule for the upper layer

  • ratiolower (dict) – Same as ratioupper but for the lower layer

  • waterbuff (float) – The z-dimension size of the water box above and below the membrane

  • platform (str) – OpenMM platform on which to run the minimization/equilibration (‘CUDA’, ‘OpenCL’, ‘CPU’, or ‘Reference’)

  • minimize (int) – If not 0 it minimizes the membrane for the given number of steps

  • equilibrate (float) – If not 0 it equilibrates the membrane for the given number of nanoseconds

  • outdir (str) – A folder in which to store the output PDB files

  • lipidf (str) – The path to the folder containing the single-lipid PDB structures as well as the lipid DB file

  • forcefield_files (list[str] or None) – OpenMM ForceField XML files used to parameterize the membrane during minimization/equilibration. Defaults to AMBER Lipid17 + TIP3P (["amber14/lipid17.xml", "amber14/tip3p.xml"]).

  • seed (int or None) – Seed for the numpy global RNG. If provided, the build is reproducible (lipid conformer choice, initial rotations, and the LJ-fluid Halton shuffle). The OpenMM minimization/dynamics step is not seeded here.

  • solute (Molecule or None) – Optional pre-positioned solute (typically a protein) around which the membrane is built. The solute must be aligned with bilayer center at z=0; the membrane is shifted in XY to follow the solute’s membrane-embedded COM. The user’s Molecule is not modified.

  • timestep_fs (float) – Integrator timestep in femtoseconds for the OpenMM equilibration. Default 2.0 (compatible with constraints=HBonds).

  • head_z (float) – Half-bilayer head-plane Z (Angstrom). Every lipid head is placed at +head_z (upper leaflet) or -head_z (lower) regardless of species, so a mixed bilayer starts with a flat head plane that NPT relaxes to per-species depths. Default 15.0.

  • head_restraint_k (float) – If > 0, apply a harmonic z-restraint of strength head_restraint_k (kJ/mol/A^2) to each lipid head atom toward its initial head plane during minimization and equilibration. Default 0.0 (no restraint).

Returns:

mol – The resulting membrane including surrounding waters

Return type:

Molecule <moleculekit.molecule.Molecule

Examples

>>> lipidratioupper = {'popc': 10, 'chl1': 1}
>>> lipidratiolower = {'popc': 8, 'chl1': 2}
>>> width = [50, 100]
>>> res = buildMembrane(width, lipidratioupper, lipidratiolower)
htmd.membranebuilder.build_membrane.listLipids()#

Lists all available lipids

Examples

>>> from htmd.membranebuilder.build_membrane import buildMembrane
>>> build_membrane.listLipids()
---- Lipids list: ...
htmd.membranebuilder.build_membrane.wrapping_dist_python(coor1, coor2, box)#
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