In general, the harness script is called by the FRESHS client with command line arguments, which are constructed by the client from the server message and can contain user-defined elements (see the configuration files for more details). For calculating trajectory fragments, the harness script should include the following elements:

• A parser for the command line arguments
• An equilibration/initial_config routine to set up the system
• A save_snapshot routine for saving the complete system state
• A load_snapshot routine for loading a full system snapshot
• A calculate_rc routine for calculating the reaction coordinate

Here is an example for a GROMACS harness script using FFS, written in BASH. The additional files can be downloaded here.

Here is an example for an ESPResSo harness script using FFS, written in TCL.

Here is an example for a FFS LAMMPS harness script using the pythonlib of LAMMPS. This script can analogously be converted to a compiled C++ simulation script, if LAMMPS is not used as python library.