normal inverse bilayer?

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3 weeks 2 days ago #7938 by di_jin
di_jin created the topic: inverse bilayer?
(Apologise if this is a duplicate. Wasn't sure if the previous one went through)

I followed the tutorial for self-assembly of lipid bilayer ( www.cgmartini.nl/index.php/tutorial/37-t...al-lipids-new-lipids ), but the results showed a head-to-head bilayer instead of a tail-to-tail bilayer. I have run the simulation several times and they all converged to the same configuration. Can anybody explain what went wrong?

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3 weeks 1 day ago #7939 by bart
bart replied the topic: inverse bilayer?
Did you add water?

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3 weeks 17 hours ago #7940 by di_jin
di_jin replied the topic: inverse bilayer?
Yes. 768 water molecules following the tutorial

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2 weeks 5 days ago #7941 by riccardo
riccardo replied the topic: inverse bilayer?
If water is there, it is very hard to believe that the lipids assembled in an inverse bilayer where the very hydrophobic tails are exposed to water. Can you post a snapshot?

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2 weeks 5 days ago #7942 by di_jin
di_jin replied the topic: inverse bilayer?
I had the identical results shown in this video posted by someone else: www.youtube.com/watch?v=SbWh_XgCHywcom/watch?v=SbWh_XgCHyw

water comes to the center between the hydrophilic heads

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2 weeks 5 days ago #7943 by riccardo
riccardo replied the topic: inverse bilayer?
Don't forget that the system is periodic in all the dimensions. This means that the upper lipid tails you see in the video "pointing towards the vacuum", are actually in contact with the tails of the lower part of the simulation box. So, lipids tails are in contact, and water it's between the polar heads: everything is fine.
Whatever software you are using for the visualization, just find the option to replicate the box in all directions and this will be very evident.

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2 weeks 1 day ago #7944 by di_jin
di_jin replied the topic: inverse bilayer?
Thank you very much!

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