Update FEP Protocol

[saratk1]

Description

Until now we have provided a specific number of switches for running FEP (instantaneous switching) and conformations have been selected randomly from the provided pool of equilibrium samples. In this PR this will be changed: There is still an option in the FEPProtocol to provide a specific nr_of_switches. If this option is chosen, the conformations will be selected randomly. If nr_of_switches is not provided, all equilibrium samples (reference_samples and/or target_samples) will be used for calculating \Delta U.

Todos

• [x] adjust the switching procedure in neq.py
• [x] add test
• [x] adjust switching script for HiPen systems

Status

• [x] Ready to go