- Posts: 30
vesicle formation
- msaeedi
-
Topic Author
- Offline
- Junior Boarder
Less
More
10 years 7 months ago #1922
by msaeedi
vesicle formation was created by msaeedi
Hi, I have a question about formation a vesicle.
I did dppc vesicle formation in example section. After 1 micro second mdrun, the bilayer is formed. I followed this simulation but it remained without any change for other 5 micro seconds. This bilayer doesn't have any curvature. I don’t know why did not formed. I used –rdd 1.4nm when I run simulation. Please help me to do a prosperous vesicle formation.
I did dppc vesicle formation in example section. After 1 micro second mdrun, the bilayer is formed. I followed this simulation but it remained without any change for other 5 micro seconds. This bilayer doesn't have any curvature. I don’t know why did not formed. I used –rdd 1.4nm when I run simulation. Please help me to do a prosperous vesicle formation.
Please Log in or Create an account to join the conversation.
- Clement
-
- Offline
- Admin
Less
More
- Posts: 211
10 years 7 months ago #1939
by Clement
Replied by Clement on topic vesicle formation
If your box isn't large enough, your bilayer is gonna be stabilized by the periodic boundaries conditions. Enlarging your box could force the bilayer to form a vesicle/micelle; but remember it's a rare event! The energy barrier must be passed in a specific way (the curvature must be right).
What are you studying? The formation of a vesicle, or do you want an already formed vesicle to run other simulations with it? For the second case, we have some conformations available; you can adapt them for your study.
What are you studying? The formation of a vesicle, or do you want an already formed vesicle to run other simulations with it? For the second case, we have some conformations available; you can adapt them for your study.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
10 years 7 months ago #1940
by djurre
Replied by djurre on topic vesicle formation
It might not be easy and straight forward. A few criteria your system should full fill:
- After the bilayer has formed, it should not be continuous over the period boundary. If it is, you box is to small, start with more water.
- I don't know what pressure coupling you used, make sure it is isotropic.
- Next there are two states a piece of bilayer can be stable in: flat (at the edges lipids will "tilt" to form a rim) or vesicle (the edges curle up to meet each other). Which one it will end up in depends on the balance between the line tension energy of the open edge and the curvature energy. Both will depend on the lipid type you use, so depending on which type you use your bilayer patch has to have a certain minimum size.
- After the bilayer has formed, it should not be continuous over the period boundary. If it is, you box is to small, start with more water.
- I don't know what pressure coupling you used, make sure it is isotropic.
- Next there are two states a piece of bilayer can be stable in: flat (at the edges lipids will "tilt" to form a rim) or vesicle (the edges curle up to meet each other). Which one it will end up in depends on the balance between the line tension energy of the open edge and the curvature energy. Both will depend on the lipid type you use, so depending on which type you use your bilayer patch has to have a certain minimum size.
Please Log in or Create an account to join the conversation.
- msaeedi
-
Topic Author
- Offline
- Junior Boarder
Less
More
- Posts: 30
10 years 7 months ago #1967
by msaeedi
Replied by msaeedi on topic vesicle formation
Hi, thanks for your responses.
I did formation of the lipid vesicle in the example section. I inserted 877 dppc and 61552 cg water in the 21nm cubic box. I see now the box in the example section is octahedral and my box is cubic and I know the shape of the box effects on the pbc. Do you think if I changed the shape of the box, the vesicle is formed or i should to enlarg the box?
thanks.
I did formation of the lipid vesicle in the example section. I inserted 877 dppc and 61552 cg water in the 21nm cubic box. I see now the box in the example section is octahedral and my box is cubic and I know the shape of the box effects on the pbc. Do you think if I changed the shape of the box, the vesicle is formed or i should to enlarg the box?
thanks.
Please Log in or Create an account to join the conversation.
- djurre
-
- Offline
- Admin
Less
More
- Posts: 272
10 years 7 months ago #1969
by djurre
Replied by djurre on topic vesicle formation
I'm not sure. It would certainly help, but it might not be enough. The vesicle might have been formed in a bigger system and later water has been removed. It might also have been setup with a script has clement suggests.
Please Log in or Create an account to join the conversation.
Time to create page: 0.097 seconds