Justification of these force fields? If it's that MBAR can be used to perform a parameter scan, justify doing something that isn't a parameter scan.
Want to make sure all the comparison are as much apples-to-apples as possible. i.e. use the same amount of data (ideally, the same data!)
I like mentioning the importance sampling from the mixture distrubution part - it's a little easier to understand.
They can be estimated analytically, but if computer time available, bootstrap is better. NOTE: bootstrap can be done trivially on histograms as well - and that's better (at fixed cost) to running 5 simulations and taking the std.
Can be generalized to more complex systems (cite Levi's work) but a pain.
Statistically indistinguishable if there is enough data and bins are well chosen.
What do you see as the main scientific point to this part [estimating Potoff, NERD from TraPPE, etc.]?
Should quantify in terms of N_eff, i.e. expain why the difference. Will also explain how to correct if needed.
Doing it with both sigma and epsilon, or just a single overall scaling parameter?
This could be too much data to ask people to keep. Maybe just ensure that all programs are compatible with outputing configurations and reevaluating energies rapidly from stored configurations.
Here are @mrshirts comments for the outline: