# Ions moving into vacuum region in slab simulation with ewald-geometry = 3dc and walls **URL:** \ **Category:** User discussions\ **Created:** [October 30, 2025, 8:37am UTC](https://gromacs.bioexcel.eu/t/ions-moving-into-vacuum-region-in-slab-simulation-with-ewald-geometry-3dc-and-walls/12850 "2025-10-30T08:37:19Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![simil](https://avatars.discourse-cdn.com/v4/letter/s/958977/32.png) [@simil](https://gromacs.bioexcel.eu/u/simil)\ **Post date:** [October 30, 2025, 8:37am UTC](https://gromacs.bioexcel.eu/t/ions-moving-into-vacuum-region-in-slab-simulation-with-ewald-geometry-3dc-and-walls/12850/1 "2025-10-30T08:37:19Z")
GROMACS version:2023.1 GROMACS modification: Yes/No Here post your question Dear GROMACS users, My system consists of graphene slab and ions (Zn, SO4 etc) on one side of slab, with vacuum in the z-direction (~30 nm). However, during the simulation, I observe that ions gradually move into the vacuum region instead of remaining near the slab surface. I would appreciate any suggestions or insights on the possible reasons for this behavior. ![2](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/40f6dc554617c80ae0e9e5aefb138fecb10a8e8b.png) I am running a slab simulation with explicit walls using the following setup in my .mdp file: ; Freeze Sheets freezegrps = metals ;MP and MW are grouped as metals in the index file freezedim = Y Y Y ; Run parameters integrator = md ; leap-frog integrator nsteps = 1000000 ; 1ns 1000ps dt = 0.001 ; 1 fs ; Removing CM Translation and Rotation comm\_mode = linear comm\_grps = system ; Output control nstxout = 1000 ; save coordinates every 1.0 ps nstvout = 1000 ; save velocities every 1.0 ps nstenergy = 1000 ; save energies every 1.0 ps nstlog = 1000 ; update log file every 1.0 ps ; Bond parameters continuation = no ; first dynamics run constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system ; two coupling groups - more accurate tau\_t = 0.1 ; time constant, in ps ref\_t = 298.0 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xy ; 2-D PBC ewald-geometry = 3dc nwall = 2 wall-atomtype = MW MW wall-type = 12-6 ;rlist = 1.4 verlet-buffer-tolerance = 0.005 ; Velocity generation gen\_vel = yes ; assign velocities from Maxwell distribution gen\_temp = 298.0 ; temperature for Maxwell distribution gen\_seed = -1 ; generate a random seed * * * ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [November 4, 2025, 3:27pm UTC](https://gromacs.bioexcel.eu/t/ions-moving-into-vacuum-region-in-slab-simulation-with-ewald-geometry-3dc-and-walls/12850/2 "2025-11-04T15:27:06Z")
Is your system net neutral? I think this behavior is affected by the boundary condition at infinite. My guess is that the ions will be close to the surface when you use epilson-surface=1.