normal Branched fatty acids and multiple minima angles

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11 years 10 months ago #981 by ScottPendley
Good afternoon,

I trying to develop MARTINI parameters for some PSI-associated molecules: alpha-chlorophyll-a, beta-carotene, phylloquinone, etc. In some of these molecules they have fatty acid tails that have multiple branch points. Using all-atom MD dihedral analysis of the fatty acid tails, I see a few of them have multiple minimas. In all-atom MD, modeling of the dihedral would involve the use of multiple sinusoidal terms to represent all the minima. With converting this molecule to MARTINI the dihedral will become an angle term which is modeled as a harmonic oscillator with a single minimum. Can anyone give me any suggestions of how best to represent this situation?

Thank you,

Scott

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11 years 9 months ago #984 by djurre
Probably won't be easy to get it perfect. You can define multiple angels (with different minima/force constants) on the same three atoms. However, this might worsen the stability a lot. Sometimes, that improves again by adding extra exclusions. And at some point you have to decide it is a coarse grained system and you won't get everything perfect...

btw: In the lab we are currently working on parameters of some of the cofactors (chlorophyll-a and beta-carotene).

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