Add [10.1021/jacsau.4c00276] polymers to the polyply library

marrink-lab / polyply_1.0

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

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Add [10.1021/jacsau.4c00276] polymers to the polyply library #378

Open ricalessandri opened 3 weeks ago

ricalessandri commented 3 weeks ago

Contributing the 3x phthalimide-containing polymer models (PMAP, PEPP, PVBP) developed in this recent paper to the polyply library.

As part of this, I'm also starting to use common termini, e.g., the same CH3 termini.

Things left:

[x] add new polymers to the library md doc
[ ] remove the previous CH3.ff and update the PTMA model so that it uses the new one; probably, we'll have then to update the PTMA test
[ ] add tests for the new polymers

ricalessandri commented 3 weeks ago

Right, that makes sense. Does https://github.com/marrink-lab/polyply_1.0/pull/327 handle this automagically? My itp_to_ff version does not. I could do it by hand for these 3 polymers.

fgrunewald commented 3 weeks ago

@ricalessandri yes, but there are some edge cases I haven't considered yet. For example, when CH3 is bound to acrylate either via the backbone or via the oxygen.