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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, ff=None, topo=None, param=None, build=False)#

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) – The platform on which to run the minimization (‘CUDA’ or ‘CPU’)

  • 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 psf and pdb files

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

  • ff (list[str]) – AMBER forcefield files for lipids

  • topo (list[str]) – AMBER topologies for lipids

  • param (list[str]) – AMBER parameters for lipids

  • build (bool) – Build system with teLeap. Disable if you want to build the system yourself.

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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