GROMACS version:2023.1
GROMACS modification: Yes/No
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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.
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
