Separation of running simulations and analyzing simulations

[tlfobe]

@cwalker7, @covo6734, and I talked about this in our meeting last Friday (May 22nd). We asked if it would be useful to separate the analysis and running of simulations?

For a lot of the current analysis scripts, simulations are run and analyzed in the same file. Many of these scripts then also have logic in them where they can read previous simulation data from the outputs directory if it exists. I feel like this makes it confusing as to what exactly is happening when a script is run.

I think if we separate analysis from simulations, we would be more flexible with what we could do with a single simulation. I think this also asks the question, what is a good file system structure for keeping simulation output and analysis output organized?

[mrshirts]

I did a bit of change of this in cg_openmm, with running and analyzing separated. Turns out this helps for parallelization as well: shirtsgroup/cg_openmm#16

[mrshirts]

what is a good file system structure for keeping simulation output and analysis output organized?

This is a good question to keep thinking about