Support for different protein conformations in the protocol

[ijpulidos]

Support for different protein conformations in the protocol would be desirable for some of our users. for the Non Equilibrium Cycling or Switching this can be done just by allowing different protein conformations in the protocol. We are now forcing the protein component to be the same here.

As long as we have a protocol that allows for different protein conformations we should be good to go in terms of the code.

There are some concerns about bookkeeping that we might need to consider, for example what if there are big clashes or the conformational changes are "too big".

[ijpulidos]

This is probably related to implementing switching in #65