normal vesicle simulation

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10 years 1 month ago #3501 by msaeedi
vesicle simulation was created by msaeedi
Hi Dear,
I wanted to study the interaction of protein with dppc vesicle, so I used dppc.gro file. This vesicle is in the octahedron box and I moved it in the bigger cubic box. I simulated vesicle, but after equilibration vesicle for 10 ns, the interior layer deform and it is like a spheroid . also, I use g_rdf command to get radial distribution function of vesicle and the interior pick is very noisy. What is wrong? Should I simulate it in the octahedron box? What can I do to have a regular vesicle during simulation.
Thanks in advance

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10 years 1 month ago - 10 years 1 month ago #3502 by Clement
Replied by Clement on topic vesicle simulation
Moving from an octahedron to a cubic box will supposedly not affect the geometry of the vesicle in such ways... If you obtain a potato from a spheric conformation, it means the vesicle isn't equilibrated. You need to force the flip-flop between layers somehow. You can do that by applying a cylindric potential, repulsive towards the tail beads of your lipids for instance, passing through your vesicle; you can run that with: Gromacs/MFFA (explanation, tutorial and everything you need). It will allow the free flip-flop and the equilibration of the inner/outer layers.

A vesicle is never completely spherical; only on pictures... Bilayer wobbles a lot during simulations, large undulations are observed, especially if the vesicle isn't totally equilibrated. Moreover, 10 nanoseconds is definitely not enough to conclude anything on the equilibration state of the vesicle. Simulate it for a couple microseconds, it might go back to its spherical geometry.
Last edit: 10 years 1 month ago by Clement.

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