The user provided input for Q-RepEx is purposely short in order to ease functionality. An example input is shown below: python repex_v1.0.py fep_ 10 5 where repex_v1.0.py is the name of the current version of Q-RepEx, fep_ is the base filename, 10 is the number of λ windows to use in the EVB-FEP/US simulation and 5 is the number of consecutive runs to be performed. This can then be user modified to be adapted to the individual runs. The base filename has to be used for the input, output, trajectory, restart and energy files.