normal membrane folding using dry MARTINI force field

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4 years 1 month ago #5683 by yuxiang900599015
membrane folding using dry MARTINI force field was created by yuxiang900599015
Dear all,

I was trying to repeat lammelar to membrane experiment in dry martini paper pubs.acs.org/doi/pdf/10.1021/ct500477k (pg 269-270)
My system consists of a membrane consists of 831 POPC lipids and was equilibrated under NVT ensemble in a large enough simulation box for approximately 600ns. The temperature was kept at 310K, approximately 40 degree higher than the transition temperature of POPC. According to the description in paper, the POPC bilayer should form a vesicle in 100 ns under same temperature.

I am using Lammps rather than Gromacs. And everything else is kept same as in the paper.
And I'm using the latest force field for the POPC lipid.

I'm wondering what could I possibly miss for this experiment.
For instance, should I apply an external force to membrane to make it curl first and then equilibrate it?

Best,
Sean

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4 years 1 month ago #5703 by jaakko
Hi Sean,

Sorry for the late reply. You shouldn't need an external force to curl the membrane. Two first things that come to mind: What happens in your simulation and what do you mean when you say large enough box? Are the edges of the bilayer free?

- Jaakko

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1 month 2 weeks ago #8606 by CharlyE
Hello,

I'm having a very similar problem here.

I'm starting from a 128 lipids bilayer equilibrated using pcoupl semiisotropic. I get a correct APL and everything is fine. I'm using Gromacs 5.

Then using gmx genconf I multiply this box by either (x y z): 3 2 1 or 6 1 1, to obtain a rather "squared" or "linear" planar bilayer patch, that I place into a box of 100x100x100 nm (bilayer edges will never see each other) and run in NVT for 500+ ns.

This is the linear starting patch after equilibration:

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At best, I obtain a slightly curled, round bilayer patch but it never transition into a vesicle. Whether I start from "squared" or "linear" bilayer patch.

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I believe the MDP parameters I'm using are all good with respect to either recommended MDP for DRY and what was done in the DRY MARTINI paper.

I tried using sd integrator with tau-t = 2 or 4, pcoupl = no, velocities are generated where necessary and temperature at 310K, otherwise I did not touch the recommended MDP parameters. I also tried the MDP of the RUN from the last mitochondria Nature Comm paper, I always get the same result.

Could you please suggest what is going wrong here ?

I'm wondering also if something fundamental did not change between Gromacs 4.6 and 5 (I'm using v5), having an effect for this specific experiment. I obtain the same results using either DRY MARTINI 2013 (POPC 13 beads version) or 2016 (POPC 12 beads version).

I also have to run with small timestep for this to be stable (5 fs), even after long equilibration.

Best,
Charly

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