BioSimSpace.Box¶

The Box package contains tools for generating parameters for different simulation boxes. This is particularly useful when needing box magnitudes and angles for generating BioSimSpace.Solvent boxes.

To support triclinic boxes that work across the range of molecular simulation engines that support, we represent the triclinic space in reduced form, using the approach documented in Appendix A of Chapter 3 from “Molecular dynamics of sense and sensibility in processing and analysis of data” by Tsjerk A. Wassenaar.

Functions¶

`boxTypes`()	Return a list of the supported box types.
`generateBoxParameters`(box_type, image_distance)	Generate parameters for the named box type with specified image distance.
`cubic`(image_distance)	Generate parameters for a cubic box.
`rhombicDodecahedronSquare`(image_distance)	Generate parameters for a square rhombic dodecahedron.
`rhombicDodecahedronHexagon`(image_distance)	Generate parameters for a hexagonal rhombic dodecahedron.
`truncatedOctahedron`(image_distance)	Generate parameters for a truncated octahedron.

Examples

Generate the lattice vectors and angles for a truncated octahedron of 10 nanometer lattice separation.

import BioSimSpace as BSS

box, angles = BSS.Box.truncatedOctahedron(10 * BSS.Units.Length.nanometer)