I have a few questions regarding the online generator for Dual topologies for free energy calculations.
Does this generator also include the use of a water model (tip3p)? If not, how would I account for this? I ask this because the tutorial on http://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/index.html states that I can do the first three steps using the generator at this link http://pmx.mpibpc.mpg.de/contact.html, and one of the three steps mentioned involves assigning the water model for simulations. So, would I have to include the water model of interest manually before/after using the generator, or does the generator account for this already?
The pmx tutorial ( the first link mentioned) is for comparing folding stabilities, but can it also be used to analyze the stability of loop closure? If so, what modifications would I need to do to this tutorial for such purpose?