Add PTMA GBNO2 IBI model to polyply library [10.1021/acs.macromol.3c00141]

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 PTMA GBNO2 IBI model to polyply library [10.1021/acs.macromol.3c00141] #343

Closed ricalessandri closed 9 months ago

ricalessandri commented 11 months ago

This is the last model to be added from 2209.02072/10.1021/acs.macromol.3c00141. It is the CG model made via Iterative Boltzmann Inversion (IBI) CG model that uses the "GBNO2" mapping. Also for PTMA.

[x] .ff; incl. link to zenodo via [info]
[x] library.md
[x] test

ricalessandri commented 11 months ago

@fgrunewald all done here too. This makes for the 4th PTMA model in polyply:

oplsaaLigParGen/PTMA.ff --> https://github.com/marrink-lab/polyply_1.0/pull/276 martini3/PTMA.ff --> merged already ibi_CGM3/PTMA.ff --> https://github.com/marrink-lab/polyply_1.0/pull/279 ibi_GBNO2/PTMA.ff --> https://github.com/marrink-lab/polyply_1.0/pull/343

A final question may be, do you like how I have arranged the 2 IBI models in the new ibi_CGM3 and ibi_GBNO2?

ricalessandri commented 9 months ago

Also done, as in https://github.com/marrink-lab/polyply_1.0/pull/279#issuecomment-1761753366.

ricalessandri commented 9 months ago

@fgrunewald I resolved the conflicts that had arisen due to the merging of the other, PTMA-related PR.