Dr. Fabian Grunewald

there is also gromacs wrapper which potentially is a better option

So this is from our friends the virtual-sites again. Because VS construct edges from all the constituting atoms it creates artificially short paths between neighbors that otherwise wouldn't be connected.

This is not really a bug but also something not so obvious. Virtual-sides make edges when the `[edges]` directive is given. This however screws with the exclusion algorithm when VS...

I think that is a good idea. Do you feel up for giving it a try to implement these parameters or shall I? Also the polyply regression tests has the...

For now I fixed the link but again implementing this recommended FF is good practice anyways

@ricalessandri this could be interesting for you. I've made a wrapper around gen_coords, called gen_replicas. It works in the same way and has the same arguments as gen_coords. However, you...

problem with the current node removal is that it involves looping, copying and modifying the large interactions dict. So you wouldn't want to remove too many nodes. For now this...

we need to do some bench marking before merging this

If you want to typehint this completely (optional), you can do something like templates: dict[str, vermouth.molecule.Block], indicating its keys are strings and values are Blocks. You'll still need to tell...

as mentioned in the discussions this PR needs some patching to the main code