add ability to select frames for thermodynamic analysis

[cwalker7]

It would be useful to be able to skip an equilibration period (and maybe automatically determine that period from timeseries analysis), or set a stride parameter for analyzing very large trajectories, for thermodynamic analysis (expectation of native contacts, free energy of folding, heat capacity). When using an exchange frequency of 100 time steps, the .nc and pdb files combined can reach several GB pretty quickly.

I already added the stride parameter as an option to the make_pdb_replica_files and make_pdb_state_files functions - so we would have to use the same parameter wherever we parse the .nc files. Adding a starting frame would be very similar.