GROMACS version: 2018.4
GROMACS modification: No
I tried to build a double bilayer system with a lower inside water layer hydration. I used bilayer to build that system and I deleted water molecules on one side in my copy and I put copy on my bilayer and you can see a bit empty space. Is it ok or maybe I should try to put some water there? Leaving this empty space can have some influents on my results? After I run simulation my results can be appropriate. And Is it possible to solvate in a specific coordinate, for example I want to put water molecules between 4.7 and 5 z coordinates. Is it possible?
The void space will rapidly close and leave a very dehydrated interface between the two bilayers. They will interact unnaturally, I would expect.
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Simulate it and see, but your water:lipid ratio still looks quite low and there appears to be a lot of smaller spaces that will compress very quickly. What is the water:lipid ratio in the system?