While I am trying to equilibrate a monolayer with a small particle solvated with water, a gap appeared between the monolayer and the solvated small particle
Did the box dimensions change, or is it just a question of visualization? Do you expect this monolayer to be stable?
I started the equilibration with short NVT. Actually to prevent water to enter the tail region the z-dimension is 4L where L is the real z length. Yeah it should be stable
My question is, can you show the evolution of the box dimensions over time? This can be a visualization artifact, and not an actual instability. You need to give more context about what you did, what you expected to happen, and what actually happened.
Thank you for the clarifications.
Here is the xyz evaluation over time.
I expect the monolayer to become stable with water region; no water escapes the lipids head groups.
xyz.xvg (60.5 KB)
Your Z-dimension is 165 nanometers, that’s a crazy lot of vacuum. The evolution of box dimensions looks like you were using isotropic pressure coupling, which isn’t a great idea here. Is the water-vacuum interface an intended feature of the simulation? What is the system you’re trying to model?