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"Bio.B-Gen" is a command line tool to generate initial systems for biological molecular simulations. "Bio.B-Gen" was mainly designed to be used with the GROMACS molecular dynamics simulation package (http://www.gromacs.org). "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. After the system is generated and all the overlaps are resolved an short GROMACS simulation run (10-20 ps) is usually required to ensure proper relaxation of the system.
Features
- Flexible control over insertion domain: random, sphere, rectangular block, etc.
- Guaranteed number of inserted molecules;
- Predictable convergence;
- Heuristic based local minima escape strategies;
- Insertion only mode (no overlap resolution)
- Resolve overlaps only mode (no insertion)
- Stable