Better linking of prepare-tune-run on mdrun parameters #56
Description
Currently, adding mdrun parameters is sort of clickish ... IMHO the user should be able to provide these in the preparation notebook too.
And besides -nsteps, all the parameters should be applied for the tuning jobs as well, otherwise we tune something else.
Using the tpr file as identifier for a simulation is quite flexible; on the other hand, offering auxiliary tpr's (em, nvt, npt, ...) generated during preparation makes little sense. Reconsider also this design.