Protein-ligand system

[IAlibay]

As discussed in MDAnalysis/UserGuide#105 (comment), an MD simulation of a protein-ligand complex would be useful for MDA tutorials etc...

I probably have quite a few simulations of some more classic FEP benchmark systems (T4 lysozyme, BRD4, etc..) that could be uploaded (although only ~ 20 ns in length since that's what you'll usually do for an ABFE window).

That being said, it might be that a more elaborate trajectory might be more helpful here, particularly considering potential future use cases, e.g. binding site waters (density analysis code), hydrogen bonding, RMSD (ligand symmetry), etc...

If such a trajectory doesn't already exist, I'm willing to do the leg work in generating the data if we can agree on an "ideal" system.

[orbeckst]

Classical T4 lysozyme sounds good. @RMeli had some comments IIRC. Maybe @xiki-tempula also has an opinion (bridging waters?). I'll be happily leave this to you all to figure out what would be the best system. I'm happy to review the PR quickly & make a new release.

See https://github.com/MDAnalysis/MDAnalysisData/wiki/add-new-data-set for adding a new data set.

[RMeli]

4W52 seems to have two ligands, one of which is benzene. Benzene might be very useful to test symmetry-corrected RMSD in the future. For the other ligand there is one bridging water and several hydrogen bonds.

[xiki-tempula]

I'm not very familiar with the T4 lysozyme or the BRD4 system. But I think the water bridge analysis could examine the binding site waters (density analysis code) from another pespective.