normal Martini membranes permeabilize water

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1 year 4 months ago #9563 by bqAlvii
Martini membranes permeabilize water was created by bqAlvii
Hi martini forum.
I am working with membranes created by martini and I have a doubt about the results obtained.

My membranes naturally generate holes where you can see the water molecules going through them, is that okay? Is it normal for martini membranes to have that effect? Am I making a mistake?

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1 year 4 months ago #9564 by riccardo
Replied by riccardo on topic Martini membranes permeabilize water
Membranes can show spontaneous pore formation, depending on the type of lipid. So, the answer really depends on the system you are simulating. Nevertheless, Martini is notoriously not that good in pore forming, so the answer may be closer to a yes than to a no.

I would recommend following the first 2 tutorials at: cgmartini.nl/index.php/2021-martini-online-workshop/tutorials to check 1) how to correctly setup a system and 2) check that you got the the correct MD settings.

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1 year 4 months ago #9565 by bqAlvii
Replied by bqAlvii on topic Martini membranes permeabilize water
Thanks for the reply riccardo. Im wondering too if its correct see water molecules trespassing the membrane bilayer (from outer to inner or vice versa). I mean, follow the same core idea as the answer before this. Am i doing something wrong or its a normal bilayer behavior?

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1 year 4 months ago #9566 by riccardo
Replied by riccardo on topic Martini membranes permeabilize water
Please re-read my previous post, thanks!

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