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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
Apache License 2.0
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Add a library table, i.e., list of models available in the polyply library #280

Closed ricalessandri closed 1 year ago

ricalessandri commented 1 year ago

I had this idea and wanted to run it with you, @fgrunewald. It might be useful to have this somewhere for users that want to know whether a certain polymer is already in the polyply library (without having to install polyply). It could then be linked in the main README.

Let me know what you think, this is a draft so many things could be improved (including maybe automating the table generation...). But wanted to first check if this is of any interest.

fgrunewald commented 1 year ago

@ricalessandri I like the idea of the library table very much, but I would add where to find the force-field files as well as the actual name of the polymer because the abbreviation doesn't need to be unique.

ricalessandri commented 1 year ago

yes, agree that the actual name is important. What I don't understand is what you mean by "where to find the force field files"; you mean a link to the papers? Currently I thought I would put the name of the library (actually, I didn't that for "Martini 2" and "Martini 3" --> should be "martini2" and "martini3") and at the same time have the hyperlink to the actual file (if one wants to take a quick peek at the model.

ricalessandri commented 1 year ago

Missing M3 models. Will commit it later today.

ricalessandri commented 1 year ago

I think it's almost done. Two remaining points

  1. Which polymers are the following?
    • 2016H66/HEA
    • 2016H66/PAM
    • 2016H66/PMAM

(highlights the need for a table with the names :))

  1. Also, in martini3 there's also a lipid-PEO think - should we include that in the table and how?
fgrunewald commented 1 year ago

Hi Riccardo,

Table looks very good already and indeed I agree we need this.

2016H66/HEA. Poly(2-hydroxyethyl acrylate)

2016H66/PAM
Polyacrylamide

2016H66/PMAM poly(methacrylamide)

  1. Also, in martini3 there's also a lipid-PEO think - should we include that in the table and how?

I think for now not. People doing PEGylated lipids will go to the tutorial hopefully and figure it out there, together with the warning that PEG lipid interactions in M3 are not good.

ricalessandri commented 1 year ago

Done - LIBRARY.md.

ricalessandri commented 1 year ago

yep - go ahead!

ricalessandri commented 1 year ago

found a typo, hold on 1 sec

ricalessandri commented 1 year ago

Ok, fixed. Ready to be merged, @fgrunewald.