Resolve issues relating to trajectory re-generation and re-calculation of hydration free energies

[davidlmobley]

• What format should the trajectories be made available in?
• Is it OK if all of these are generated via OpenMM?
• I presume we should use the same GAFF/AM1-BCC files, including the same exact charges; we presumably want to use the new consistent mol2 files I generate with a single script from PR Implementing script to generate Bayly's preferred AM1-BCC charges #11, right?

[davidlmobley]

With respect to these:

• Format: Trajectories should be made available in something plain-text (perhaps AMBER format?) as well as something more modern, perhaps netcdf or similar. Use of libraries like netcdf can pose an activation barrier to people who are unfamiliar with them, reducing use of the trajectories, but is better in general.
• These could be generated by OpenMM, certainly.
• Yes, we want to use the same files, and exact same charges, with the consistent .mol2 files as asked above.