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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 CGM3 IBI model to polyply library [10.1021/acs.macromol.3c00141] #279

Closed ricalessandri closed 10 months ago

ricalessandri commented 1 year ago

Contributing the Iterative Boltzmann Inversion (IBI) CG model (that uses the same mapping as the Martini 3 model, a mapping dubbed "CGM3") developed for PTMA in https://arxiv.org/abs/2209.02072.

Test to follow, but first we need to figure out Discussion https://github.com/marrink-lab/polyply_1.0/discussions/278.

fgrunewald commented 1 year ago

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

fgrunewald commented 1 year ago

@ricalessandri the patching of the main code is done; with the current version on GitHub you should be able to add an info statement to your polymer on where to find the FF parameters. I suggest putting them on zenodo with a doi

ricalessandri commented 1 year ago

Great! Just waiting a bit more for the manuscript to finish peer review and then I'll act on this.

P.S. Should we remove the "wait_for_vermouth" label?

fgrunewald commented 1 year ago

@ricalessandri we are pushing the development of our RNA/DNA infrastructure. Before we are merging we are going to have one additional release and the probably a longer break for a couple of month. If you want this added into the release it has to be merged latest next week.

ricalessandri commented 1 year ago

OK, thanks for the heads-up!

ricalessandri commented 1 year ago

To Do:

ricalessandri commented 1 year ago

@fgrunewald This is also done. Let me know if I missed anything and let me know if you like the news piece.

ricalessandri commented 11 months ago
  1. As discussed, I renamed to ibi_cgm3 (lower-case). I think I did it in all the places it needed to be renamed.
  2. Yes, that works! This applies to https://github.com/marrink-lab/polyply_1.0/pull/343, too

This is now ready to go!

One final comment I have, the [ info ] seems to get printed one time per monomer. A bit redundant but not sure if this can be prevented.