I ran the NPT simulation for a membrane protein embedded in the lipid bilayer and I see that water is penetrating from one small cavity, located at the lipid-protein
interface, into the membrane (the interface with protein). I don't know if this is
expected or not. Would be so thankful if somebody helps.
To answer the question, I must pose a number of questions of my own:
How long is the simulation?
How did you build and equilibrate the system?
How large is the pocket of water, and does it destabilize the structure of the protein or lipids in any way?
Water penetration into the membrane would imply some sort of pore formation/perforation of the membrane. Is this due to the embedded protein?
Calculating the order parameter of the lipids will give you some insight as to the structure of the membrane.
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