Bas Rustenburg

A decent amount of updates have been added to the code. Would it be helpful to create a new prerelease? Since we actively use some of this code in projects,...

https://github.com/choderalab/protons/blob/master/examples/Ligand%20example/imidazole.xml#L24 @jchodera notes: For example, we have `` denote a residue, `` denotes an atom. The ` tag doesn't denote a proton, but a block of information defining parameters for...

Abl benchmarks

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 Breakdown of an Abl NCMC benchmark.

Now that we've settled on a datafile format, we should make a module that can plot the data we have. This should include ways to - [x] visualize a calibration...

Tweaks for calibration plots suggested by @jchodera * make sure the figure width is set to one column (3.5 inches?) * reduce the axis label font size * increase the...

We want to pick a default - [ ] NCMC protocol ( could use linear for everything) - [ ] Desired simulation length - [ ] pH values of interest

Add new data and running scripts, and clean up files that used the old API in https://github.com/choderalab/constant-ph-systems repo, and start adding new systems to it.

We have settled and fixed most bugs in the netCDF4 format. We should automate the BAR analysis procedure.

Update the documentation.

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The documentation is out of date. Some examples would now work differently, and some code has been deprecated/removed. We should add new documentation and new examples before releasing

The code currently relies on the g_k values in the input xml files. These are assumed to be at the right value to produce the desired target weights. The user...