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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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Contribute PVA OPLS-AA/LigParGen .ff file #324

Open ricalessandri opened 1 year ago

ricalessandri commented 1 year ago

This is a self-sufficient PVA ff file. Usage example to obtain a 10-mer:

polyply gen_params -f PVA.ff  -name PVA -seq CH3a:1 PVA:10 CH3b:1 -o PVA_n10_oplsLigParGen.itp

This is currently for this discussion.

This PR also brings up a "philosophical" question IMO. Should we try to have a "generic" -CH3 termini for OPLS polymers or should we have multiple custom "-CH3" termini for PS, PVA, PEO, etc. (in which case, how do we name them given that, if one wants to use the library, each block must have a different name)?

ricalessandri commented 1 year ago

Very good point. Looking at the charges, the changes in the PVA block charges are not really significant. But indeed we should think about how to have a unique PVA block. Or, more generally, how to deal with this in general.

I agree that tackling itp_to_ff first and the fixing this PR is the way to go. I actually wanted to talk to you about itp_to_ff (also in relation with the latest GH discussion that involved this PR). I will write you an email so perhaps we can have a Zoom chat about it soon.