- Posts: 29
error when simulating bilayer
- thu nguyen
- Topic Author
- Offline
- Junior Boarder
Less
More
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
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
Please Log in or Create an account to join the conversation.
- djurre
- Offline
- Admin
Less
More
- Posts: 272
11 years 3 months ago #1358
by djurre
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...
Yes, 6 CG water per lipid gives the best shot at forming a bilayer. Of course you can use lipids.
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.
Please Log in or Create an account to join the conversation.
Time to create page: 0.089 seconds