normal charged small molecule bead mapping

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1 year 3 months ago #9594 by benzenekim
charged small molecule bead mapping was created by benzenekim
Greetings :)

I'm struggling with bead mapping, on charged molecules.

In example, if I have phenolate ion, how do I map this molecule?

I think I might use Q- beads, but I don't know which Q bead(SQ5, Q3, TQ2.. etc) I have to apply.

Is there any information or guideline that helpful while choose Q-bead types?

Thank you.

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1 year 3 months ago #9596 by vainikka
Replied by vainikka on topic charged small molecule bead mapping
Hey hey,

If you haven't done so already, check out the SI of the Martini 3 paper - it contains basic rules for bead assignments and sizes.

From the top of my head I'd start with something like TQ5n - TC5 - TC5 for your molecule, but in the end it's up to you as the user to test that your models make sense.

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