molsysmt.build.make_water_box#
- molsysmt.build.make_water_box(box, form='molsysmt.MolSys', skip_digestion=False)[source]#
Building an SPC/E water box from a reference tile, supporting triclinic cells.
This helper replicates the bundled cubic spc216.gro tile (216 SPC waters at ~300 K) to cover the orthorhombic bounding box of the target cell, then trims molecules whose oxygen fractional coordinates fall outside the requested box (which can be triclinic). The generated system contains one structure with coordinates in nanometers and a fully populated topology for three-point waters. Because the packing comes from a pre- equilibrated cubic tile, minimization and short equilibration are recommended to relax any residual overlaps.
- Parameters:
box (array-like or pint.Quantity) – Box matrix (or sequence of box matrices) with shape
(3, 3)or(n_structures, 3, 3). Only the first box is used. Supports triclinic cells; side lengths and tilt must be in nanometers.form (str, default 'molsysmt.MolSys') – Target form of the returned system. Currently returns a
molsysmt.MolSysinstance.skip_digestion (bool, default False) – Whether to skip MolSysMT’s argument digestion.
- Returns:
Water box with coordinates of shape
(1, n_atoms, 3)in nanometers, topology for SPC/E waters, and box of shape(1, 3, 3)in nanometers.- Return type: