normal membrane folding using dry MARTINI force field

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2 years 9 months 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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2 years 9 months 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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