[SepTop docs] Simulation overview unclear on if the same restraint is used between repeats

[IAlibay]

The docs state:

The :class:`.ProtocolDAG` of the :class:`SepTopProtocol <.SepTopProtocol>` contains :class:`.ProtocolUnit`\ s from both the complex and solvent transformations.
This means that both legs of the thermodynamic cycle are constructed and run sequentially in the same :class:`.ProtocolDAG`. This is different from the :class:`.RelativeHybridTopologyProtocol` where the :class:`.ProtocolDAG` only runs a single leg of a thermodynamic cycle.
If multiple ``protocol_repeats`` are run (default: ``protocol_repeats=3``), the :class:`.ProtocolDAG` contains multiple :class:`.ProtocolUnit`\ s of both complex and solvent transformations.

We should clarify if that means that when you set protocol_repeats=3 all 3 repeats use the same Boresch-style restraint.

[hannahbaumann]

It actually currently would re-calculate the Boresch-style restraints when using protocol_repeats=3.

openfe/openfe/protocols/openmm_septop/equil_septop_method.py

Line 1249 in 7584efe

for i in range(self.settings.protocol_repeats)

Is that something I should change? I think both methods have their advantages.

[hannahbaumann]

Addressed in this commit 95f8a1b

[IAlibay]

something I should change

No this is purely a docs clarification thing. We can work out if we should or shouldn't at a later date.