normal Ethanol Polarity

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1 month 2 days ago #7424 by abelessi
abelessi created the topic: Ethanol Polarity
Dear all,

I am interested in modeling how small molecules (ethanol) can disrupt lipid membranes. The effect in question relies on the polarity of ethanol molecules which can stabilize both the hydrophobic tails and hydrophilic heads of lipids in solution.

Does Martini have any implementation that can take such effects into account? I realize that the level of coarse-graining used in the Martini force-field doesn't allow for a detailed representation of ethanol molecules (i.e. it is a single polar bead) but the polar bead type doesn't discriminate between hydrophobicity/hydrophilicity.

Would it be feasible to model an ethanol molecule as a kind of 'Janus' particle composed of hydrophobic and hydrophilic halves? I have done some initial tests of such a "bi-phasic" ethanol molecule but would like some feedback from more experienced Martini users.

Any suggestions are very welcome.



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4 weeks 1 day ago #7438 by riccardo
riccardo replied the topic: Ethanol Polarity
I would not model ethanol with an hydrophilic and hydrophobic part in Martini as this means having an almost united atom model (3 non-hydrogen atoms to 2 "Martini beads") which goes way to far from the 4-atoms-to-1-bead mapping scheme employed in Martini.

You could definitely check the effect of ethanol vs octanol etc, see, for example:

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