unanswered Matching bilayer thickness between AA and CG

  • yogi@martini
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2 years 10 months ago #7549 by yogi@martini
Matching bilayer thickness between AA and CG was created by yogi@martini
Hello Experts,

I saw people use one extra bead to match the bilayer thickness (if it is underestimated) between AA and CG. For example in long tail of lipid, if there are 12 C atoms, instead of clubbing them in 4-1 to get 3 beads they club it 3-1 to get 4 beads and set them as C1 instead of C2. My question is:
1. Is it trivial to get lower bilayer thickness since the bead is nothing but the center of mass of 4 atoms, and hence will give small bilayer thickness (if it is calculated by distance between end atoms) is it the same case with the bilayer thickness calculated from electron density profile.
2. Is the above mentioned method of getting correct bilayer thickness, reasonable?
3. What if instead of making 3-1 mapping, I keep 4-1 mapping and increase the bond length between beads, that is making them ~0.6 instead of 0.47 to get correct bilayer thickness.

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