Port in plotting/analysis functionality from alchemical-analysis and yank

In recent discussions with OpenEye about free energy calculations on their Orion cloud computing platform, it became clear they will benefit from an open analysis library (alchemlyb in particular) because users are running calculations with Yank, GROMACS, and probably soon AMBER on their platform. Thus they are likely prepared to invest some developer time in ensuring alchemlyb has the functionality needed. I was recently discussing this with Christopher Bayly ( @cbayly13 ) and Gaetano Calabro ( @nividic ) there and I said I’d summarize what I thought needed to be done on the issue tracker so that @nividic could begin work in the coming weeks if everyone here is on board with it.

I think the main things that I think we would want added to analysis in the short term is:

1. Overlap matrix analysis from alchemical-analysis, e.g. as in DOI 10.1007/s10822-015-9840-9
2. Mixing diagrams as seen in Yank’s simulation health reports
3. Graphs of equilibration/number of effective samples as in Yank’s simulation health reports
4. Numerical analysis of statistical inefficiency/number of effective samples in input datasets
5. Any other key features of Yank simulation health reports I’m missing? (I don’t have a report in front of me at the moment.)

Possibly also there is a need for ensuring at least a threshold minimal number of samples are retained for analysis after decorrelation.

For Orion purposes I would also suggest running multiple analysis methods (BAR, MBAR, TI) whenever the data allows for it (often) and cross-checking results for consistency; inconsistencies are usually a warning of problems.

An additional list of possible changes is on the alchemical analysis features list where we were brainstorming about this.

Tagging also @harlor for thoughts as well as @hannahbaumann and @andrrizzi . And of course @dotsdl and @orbeckst .

@nividic the way to get started would be to basically pull the relevant code from alchemical-analysis and yank (allowable by the licenses) and adapt to (improve/generalize for) this.

[mrshirts]

Cool, I’ll try to keep posted on this. Automated bootstrap error (better that the internal error estimator in most cases).

[davidlmobley]

Yes, I agree with the rest here. This is something we still want (and the lack of the functionality here means people occasionally ask me for help with alchemical-analysis and I have to decline) but it is not done yet.