normal ubiquinone/ubiquinol ring backflipping

  • denizaydin
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1 month 1 week ago #7561 by denizaydin
denizaydin created the topic: ubiquinone/ubiquinol ring backflipping
Dear Martini Users,

I have been trying to use the ubiquinone/ubiquinol parameters published in Djurre H. de Jong et al. J. Phys. Chem. B, (2015), which are available in the force fields section. After an equilibration I observe a backflipping of the ring structure. I'm wondering if the authors of the paper had the same problem, and how I could solve it. I can see in the parameter file that there is a dihedral term added which says "to prevent backflipping of the ring", but in my simulations it doesn't seem to work.

I tried to describe the problem here:

I have tried changing the parameters (either angles or the dihedrals) but did not succeed. Thanks for any helpful suggestions.


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1 month 5 days ago #7572 by Pim
Pim replied the topic: ubiquinone/ubiquinol ring backflipping
Dear Deniz,
Sorry for the slow reply, the notification system of the forum was down for a few days.
I wasn't involved in the work, but looking at the itp the situation you drew should not happen: there are exclusions between UQ2-5, 3-5 and 4-5, so they don't have non-bonded interactions with each other, and the angle 2-1-5 should prevent the situation in your drawing. However, there is also a commented '4-1-5' angle in the itp file, which makes me suspect that it may have happened in the past too. Maybe adding this angle back in prevents your bending. However, I think that the image you draw isn't necessarily an unrealistic situation, the head can move freely with respect to the tail. Is it stuck in this confirmation forever or only temporarily?

Also, I am not entirely sure, but I don't think this movement is what is meant by 'backflipping' of the ring. The dihedral with the comment is an improper, which keeps the 4 ring beads flat. I think what happened was that the 4 atoms folded up without it, like if you would fold two opposite corners of a square piece of paper together and this needed to be prevented. The beads on opposite 'corners' of the ring are not excluded from each other, so their non-bonded interaction would make this folding happen if the dihedral wasn't there.

Hope this helps,

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