JenkeScheen

Thanks Lester, this is definitely helpful for now. I agree that simplifying commandline input would offer a lot of additional flexibility

Linking this thread with [my working repo](https://github.com/michellab/bss_fep_advanced_tut_bg).

Hi @ppxasjsm if you've done any work on LOMAP network generation to show within a notebook that would be very helpful! It's starting to look like the LOMAP build I...

I'm just going to build a networkx function that takes [the edges text file written by LOMAP](https://github.com/michellab/bss_fep_advanced_tut_bg/blob/main/outputs/lomap/out_score_with_connection.txt) and creates a simple neato graph while loading molecule images and LOMAP scores...

the graph generation yes, getting to the line requires some more work (rdkit to load molecules, draw images correctly + save, etc)

update: I've now pushed a [working notebook](https://github.com/michellab/bss_fep_advanced_tut_bg/blob/main/fep_workflow_ros1.ipynb) that runs LOMAP on a set of ligands, then uses networkx to plot LOMAP's output and finally uses BSS to setup SOMD folders...

I have now added a draft slurm submission script (of course the BSS functionality of loading a SOMD environment still has to be added for this) [the main setup notebook](https://github.com/michellab/bss_fep_advanced_tut_bg/blob/main/fep_workflow_ros1.ipynb)...

note that this workflow doesn't have .Solvation() steps yet but that should be easy to implement at a later stage; the only bottleneck there is deciding on how we can...

for a bound FEP simulation with gromacs/20.4 (TYK2 in a 20nm waterbox) I was seeing similar behaviour on our cluster (presumably the same as @ppxasjsm is referring to). What helped...

@jmichel80 I've not been doing anything fancy, just using the same input files mostly. However, an impromptu conversion would probably look like: Write to mol2 with BSS: `BSS.IO.saveMolecules(mol_path, BSS_mol, "MOL2")`...