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Dear Gromacs users, I want to simulate the ions transport behaviors through a pore on the graphene surface. I build a periodic graphene sheet with a pore and put it in the middle of the box. The box was divided into two chambers by the graphene sheet along z axis. The upper chamber was filled with 0.5 M NaCl, the lower chamber was filled with pure water. My .mdp parameters are as follows:
integrator = md
dt = 0.001 ; ps
nsteps =100000000
comm-grps = system
comm-mode = linear
energygrps =
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10000
nstenergy = 10000
nstxout-compressed = 10000
compressed-x-grps = system
;
continuation = yes ;
pbc = xyz
periodic-molecules = yes
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = no
Tcoupl = V-rescale
tau_t = 0.2
tc_grps = system
ref_t = 298.15
Pcoupl = no
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
;
freezegrps = graphene
freezedim = Y Y Y
constraints = none
electric-field-z = -0.1 0 0 0
From the trajectory, it was observed that some Na+ ions pass through the pore from the upper chamber to the lower chamber. However, because of the periodicity, they can go across the box back to the upper chamber and pass through the pore once again.
I tried to add a graphene sheet as a piston at the top and bottom of the box, respectively, and set pbc = xy. Unfortunately, I did’t see any Na+ pass through the pore even extended the simulation time scale to 1000 ns.
Which way is correct? Could u please give me some suggestions?
Thank you very much!