Bio.B-Gen
Initial system (box) generator for biological molecular simulations
..."Bio.B-Gen" depends on the GROMACS topology and force field information (.top and .itp data files) during the generation stage.
"Bio.B-Gen" adds specified number of copies of a molecule to an existing configuration to a specified spacial domain inside the system, such as a sphere, cube, spherical shell, layer, etc. Then, optionally, "Bio.B-Gen" resolves overlaps between molecules in the system and saves the new molecular configuration. By running "Bio.B-Gen" multiple times for different molecular species and spacial domains quite complex initial systems can be generated. ...