normal Bilayer self-assembly in Martini 2

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5 months 3 weeks ago #9407 by gene_editor
Bilayer self-assembly in Martini 2 was created by gene_editor
Dear Martini developer,

I was trying to follow the martini 2 tutorial to build a dppc bilayer and its self-assembly. However, after building the random initial system and finished minimization, I do not see any equilibration steps before production. I wonder if the equilibration, such as NVT or NPT equilibration, is needed before the actually production MD simulation.

Also, will this be the similar procedure (minimization + production MD simulation) to self-assemble a lipid vesicle? Thanks in advance.

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5 months 2 weeks ago #9422 by vainikka
Replied by vainikka on topic Bilayer self-assembly in Martini 2
Hi,

Running equilibration steps is always recommended; the tutorial I think you are referring to has a section this, where the self-assembled bilayer is equilibrated using semi-isotropic pressure coupling.

As to self-assembling a lipid vesicle: Are you studying the self-assembly, or do you just want a vesicle? In the latter case, check out the CHARMM-GUI Martini maker.

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