After installation, there will be the main executables in $MBX_HOME/bin/.

  • single_point will return the energy (Binding Energy) in kcal/mol for a given configuration. One can have multiple systems in the nrg file, and single point will return the energies of each one of them. If PRINT_GRADS is manually enabled in the source code in ($MBX_HOME/src/main/single_point.cpp) it will also print the gradients.
  • optimize will optimize a given configuration. You can optimize a single nrg system, or pass an XYZ file with a set of configurations, in which all of them will be optimized.
  • mb_decomp will compute energies for subsystems for the given system(s), then performs many-body decomposition and prints the n-body contribution for all subsystems. If the flag to skip many-body decomposition ("-e") is activated, it instead prints the binding energy for all subsystems.
  • order_frames will compute the energies for a given list of configurations from the XYZ file, and rearranges the configuration frames in the order of increasing energy.
  • normal_modes will compute the normal modes for an optimized nrg file. Requires the GSL library.