This will stay distinct from nonequilibrium-gilsonlabucsd, which should remain as the "publicly" available version of the code.

• Make new directory nonequilibrium-master on local.

• Inside nonequilibrium-master/ create...

  • manuscript for files from nonequilibrium-manuscript. These are similar to -- but not exactly the same as -- the files in nonequilibrium-gilsonlabucsd. They contain additional explorations that did not make it into the final manuscript. Now this is in code/, copied there using rsync -au

  • literature for files from nonequilibrium-literature-review. These are Markdown files with associated build CI build scripts modeled after deep-review.

  • explorations for files from nonequilibrium/nonequilibrium-explorations. These contain notebooks for PDB searching and achiral to chiral transitions.

  • md-data for the raw simulation data (excluding trajectories, which are stored in large-file-storage on Kirkwood and GPFS).

  • code filled with nonequilibrium/code/SG-model-v2, nonequilibrium/code/torsion-individual, and nonequilibrium/code/torque-scans copied with rsync -au.

Now, there needs to be a good way to store the code. There is code from the manuscript, and code from just before making the manuscript, and then much older code.

There are still several side projects that could be merged:

• The torsion-individual that...
• The torsion-scan that ...
• The shiny web app
• The old Brownian dynamics code