System is distroted on applying dc electric filed

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1

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Dear users,
I am applying an electric field of 1.5 V/nm along the Z-axis to a system with a liquid-liquid interface. The system has the interface aligned perpendicular to the Z-axis, but after the MD simulation, the interface becomes aligned parallel to the Z-axis. md.mdp is :
title = OPLS Lysozyme NPT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 100000000 ; 2 * 500000 = 1000 ps (1 ns)
dt = 0.001 ; 2 fs
; Output control
nstxout = 0 ; suppress bulky .trr file by specifying
nstvout = 0 ; 0 for output frequency of nstxout,
nstfout = 0 ; nstvout, and nstfout
nstenergy = 10000 ; save energies every 10.0 ps
nstlog = 10000 ; update log file every 10.0 ps
nstxout-compressed = 10000 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = no ; Restarting after NPT
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
; Neighborsearching
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
electric-field-z = 1.5 0 0 0
; Temperature coupling is on
tcoupl = nose-hoover ; modified Berendsen thermostat
tc-grps = system ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; Apply pressure coupling separately in X-Y and Z
tau_p = 5.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; Velocity generation is off

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Are there any modification needed in the mdp file? Could anyone help with the issue?

Thank you

2

With a liquid system, the electric field in enhanced by a factor of the dieletric permittivity when using PME with epsilon-surface=infinity. You need the scale down the applied field by the dielectric permittivity. Alternatively you can set epsilon-surface=1, but that will suppress the fluctuation of the dipole of the system by the same factor.

Still you might see get the conformation you see. If the gain in electrostatic energy is higher than the cost of the extra interface area, that is the lowest free-energy state.

PS: Your have a too coarse PME grid. You should use fourier-spacing=0.125 with a cut-off 1 and pme-order=4.

3

Dear @hess
Thank you for your response. I will follow your suggestion.

I have one more concern: do we need to add any electrodes to the system manually, or will the simulation automatically assign the positive and negative electrodes? In several papers, I have seen references to the movement of positive and negative electrodes, but the figures do not explicitly show any added electrodes.

4

Using electrodes is a completely different way of applying an electric fields. I think you need to do some background reading.

5

okay sir. I will try this. Thank you