unanswered Martini 2 vs Martini 3

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1 month 2 days ago - 1 month 1 day ago #9141 by peter
Martini 2 vs Martini 3 was created by peter
Hello everyone,

I would like to parameterize a ligand (say Buprenorphine) and was wondering whether I should stick to Martini 2 or try Martini 3. This would be my first trial outside the VMD tutorial and hence I sincerely appreciate your feedback.

  1. Suppose if I do some simulations with Martini 2 scheme and submit a manuscript within the next 2 years, could the work get criticised for using a previous version of the Martini coarse-grain model?

  2. Should I use polarizable water during ligand parameterization if I am going to perform simulations with membrane bilayer later?
Feedback: The CHARMM-GUI currently does not support ligands. It would have been easier to set up the entire system there if it was feasible.

Thanks a lot for reading!
Last edit: 1 month 1 day ago by peter.

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