GROMACS modification: Yes/No
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Hello dear friends, I am work on membrane with a nanoparticle. Everything is OK until the energy optimization step, but in the NVT, NPT and MD steps a few molecules of water enter the membrane. Is this normal or should it not happen?
What do you mean? It is normal that water molecules are between hydrophilic lipid heads, but it is rare that they are in hydrophobic membrane core. It is possible, but it is rare. Water can flux across the membrane. Here you can read how they measure water flux across the membrane. https://pubs.acs.org/doi/10.1021/acs.jpcb.6b01870 It depends also on temperature - higher temperature - more water can enter the membrane. Remember that when you build the system to delete all the water molecules which are in the hydrophobic part of the membrane and then minimize energy and equilibrate. In my opinion, it is possible, but water molecules inside a membrane spend a very, very short time because they “don’t like hydrophobic environment”. If you see that they are there all the time something is wrong. Maybe your topology is wrong or your initial configuration. You can delete these water molecules which are inside your membrane and try to rerun your simulation.
thanks for your response