I am simulating a CG system of graphene and Protein with polarizable water using Martini/Gromacs. During equilibration I looked at the trajectory using VMD and it appears that the PW particles are permeating through CG-graphene sheet.
the system was prepared with standard set except I solvated the system directly with PW (16210(protein beads)+ 1317405(PW beads) + 19504(grahene beads)+ 11176(ions)) in a 45nm x 45nm x 30nm box.
I have to use the PW because normal martini water model is layering across the simulation box (2 layers every 1 nm distance).
Could anyone help me out in understanding why this is happening?? as well as how to solve this issue??