Oliver Beckstein

@cadeduckworth is H-bond analysis something that you'd want to complete for a MDPOW paper?

Yes, that sounds like a logic error in the code.

@ianmkenney can you please take a look together with @VOD555 ?

We can also add pybol code from https://github.com/ianmkenney/PyBOL into our tests (to get rid of one package dependency with unmaintained code) and then replace it eventually with simpler code.

In the meantime, we're updating pybol where necessary and wait for 0.3.0 https://github.com/ianmkenney/PyBOL/issues/25

Lots of conflicts to resolve, @cadeduckworth !

The manual workflow as shown is a good mini tutorial and looks already very good. Presenting the data will be more of a challenge—the distance KDEs are naturally cut off...

The distance histograms are interesting. You can see how molecules start to overlap with the disappearing solute.

For the S08 data, the number of solvent atoms is initially 60,000 — there aren't that many waters in the box, are they? Can you do the following calculation: Given...

I am not sure if the time series contain more interesting information than the averages or distributions — at least in equilibrium. Time series in equilibrium are good as a...