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ricalessandri / Martini3-small-molecules

Martini 3 small-molecule database
https://doi.org/10.1002/adts.202100391
Apache License 2.0
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Inaccurate statements in the tutorial #4

Open ricalessandri opened 2 years ago

ricalessandri commented 2 years ago
  1. In the tutorial - both in the repo and at cgmartini.nl - we say:

"Note that the bimodality of the distributions of the first two dihedrals cannot be captured by the CG model."

Which is not true. This should be fixed. Kudos to @paulocts for pointing this out.

ricalessandri commented 2 years ago

  1. Again in the tutorial, we say: "the number of beads should be optimized such that the maximum mismatch in mapping is ±1 non-hydrogen atom per 10 non-hydrogen atoms of the atomistic structure;". But is this really OK? What about 5-membered rings like furan? We need to mention that 5-member rings, because they need 3 beads in order to be represented as rings, thus "breaking" that principle above. Again, thanks @paulocts to bring this inaccuracy up.

    Add something like: "Exceptions incl. : thiophene and furan where 3 T-beads have a mismatch of –1 given that 5 non-hydrogen atoms are mapped onto 3 T-beads (which are parametrized to represent 6 non-hydrogen atoms)."