Nathan M. Lim comments

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                                            Nathan M. Lim

May ultimately need different handling of long range charge interactions

The option to treat this is provided [here](https://github.com/MobleyLab/blues/blob/master/blues/simulation.py#L162) With the parameter `alchemical_pme_treatment`, I'm not exactly sure what the best option to use here is but it's been set to the...

General suggestions for code cleanup/improvements

Hi @dotsdl, Before you go and refactor the code, there is currently a PR (#68) where @halx has done lots of work in refactoring the code. Nobody has had the...

[WIP] Analysis tools for identifying ligand binding modes from MD or BLUES simulations.

This will need some changes with upcoming changes to our NCMC reporter.

Make py3 compatible

I've had a converted py3 version by using anaconda's 2to3 conversion tool. There were some hiccups during conversion involving bytes/strings but I think I've handled them. Also, I've only tested...

small ligand solvation energy calculation:error:cannot compute statistical inefficiency

Hi Sanaa, since we don't have a version scheme implemented the changes would depend on when you first installed alchemical analysis. You can also view the commit log if you...

plugin not functional

I'm in the same boat. It's not totally clear or intuitive on how to just get the code of the designed page? Why can't I just export the designed page...