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normal error when simulating bilayer

  • thu nguyen
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11 years 3 months ago #1357 by thu nguyen
error when simulating bilayer was created by thu nguyen
Dear All,

I am practising tutorial 1a and 1b. But the bilayer that i got is in x-axis direction, and it's hydrophobic terminal has outward direction. What happens ?

And i don't know why we have to add 6 CG water per lipid. Is that ratio appropriate for bilayer self-assembly ? And can i choose another value of number of lipids (not 128 as the tutorial) ?

Thanks in advance !
KT

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11 years 3 months ago #1358 by djurre
Replied by djurre on topic error when simulating bilayer

thu nguyen wrote: Dear All,

I am practising tutorial 1a and 1b. But the bilayer that i got is in x-axis direction, and it's hydrophobic terminal has outward direction. What happens ?


If it is in the X-direction you can simply rotate it editconf. Do you mean the lipid tails are pointing to the water? That seems highly unlikely...

thu nguyen wrote: And i don't know why we have to add 6 CG water per lipid. Is that ratio appropriate for bilayer self-assembly ? And can i choose another value of number of lipids (not 128 as the tutorial) ?


Yes, 6 CG water per lipid gives the best shot at forming a bilayer. Of course you can use lipids.

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