unanswered Ubiquinone/ubiquinol ring backflipping

  • denizaydin
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2 years 4 months ago #7564 by denizaydin
Ubiquinone/ubiquinol ring backflipping was created by denizaydin
Dear Martini Users,

I have tried using the ubiquinol/ubiquinone parameters from De Jong et al, J. Phys. Chem. B, (2015), which is available on the Martini website. After an equilibration and a short production, I observe the backflipping of the ring on all 4 copies of the molecule for multiple runs of the simulation. I saw in the itp file that there is a dihedral with a note "to prevent backflipping of the ring", but I still observe backflipping.

I tried to depict the situation in this image:

And also a pdb file of the final frame can be found here (there are 4 ubiquinol molecules with resname UQL), where you can see that beads UQ2 or UQ3 are very close to UQ5: www.dropbox.com/s/t8v09ghdpoylpx6/lastframe.pdb?dl=0

I'm curious if anyone using these parameters observed this, and I would appreciate any help to fix this problem.

-- Deniz

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