Lester Hedges

Hi there, I believe that this was just inferred by looking at the plots above the section that you are referring to. There is an object `free_nrg0` that contains the...

Hi both, Here are a few comments: > The notebook assumes the user has access to parameterised ligands (in vacuum) that have coordinates matching those of the parameterise protein input....

Just reading this bit again... > It would be better to equlibrate the solvated ligand0:complex, and then use a snapshot after equilbration to generate the merged molecule. Yes, that would...

Hmm, there are a lot of things here that aren't currently supported and would need to be implemented / tested if we want to do this in a clean way....

To support multiple restraint types it would also make far more sense to add a restraint option that can take matching keywords, e.g. `restraint = option`, where `option = None,...

Yes, the first three bullets were effectively what I was thinking, adding some logic to go from the SLURM indexes to the specific legs. I agree that restraints are important...

No problem. BioSImSpace will autodetect the path to GROMACS so it can write it out for us when the user specifies the engine. We can get the path using `free_nrg.runner.processes[0].exe()`...

If possible, it would be good to agree on what type of restaints we want to support. In your example, I see things like the following: ``` NVT equilibration with...

I've created an issue thread for the discussion of equilibration restraints [here](https://github.com/michellab/BioSimSpace/issues/203).

The script could detect the format of the output in the directories and select the appropriate analysis tool. I guess this would provide the flexibility that we want in the...