[gmx-users] Fwd: Ionic liquid and CNTs

[Candy Deck]

Dear Gromacs Users.
I started using Gromacs few month ago.
Obviously, I need your help.
My system is composed of 2 carbon nanotubes confined between 2 graphene
sheets.
Closed to each graphene is a box of ionic liquids.

My graphene sheets are just here in order to prevent the Ionic liquid to
flow around the carbon nanotube.

I did minimise my system.
The person I'm taking over used to "freeze" the graphene and the CNT.
In my case, I use position restrain to the carbon forming the graphene and
I restrain the position of the carbon forming the CNT to a plan.

I did read that position restrain must be used carrefully as well.

I'm realising that this systems is quite complex ...
I'm tending to use a compressibility rather low (1.6e-8 bar-1) because I
read that the compressibility of Ionic liquid is much more lower than the
one of water.
after a 500 ps simulation in order to fill the CNTs, there is like a vacuum
bubble above the pore.

Does someone know what is happening ??

Thanks in advance !
Candy

here is my .mpd file :


; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.0005
nsteps                   = 1000000
; number of steps for center of mass motion removal =
nstcomm                  = 100

; LANGEVIN DYNAMICS OPTIONS =
; Temperature, friction coefficient (amu/ps) and random seed =
; bd-temp                  = 400
; bd-fric                  = 0
; ld-seed                  = 1993

; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol                    = 10
emstep                   = 0.01
; Max number of iterations in relax_shells =
niter                    = 20
; Frequency of steepest descents steps when doing CG =
nstcgsteep               = 1000

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 500
nstvout                  = 0
nstfout                  = 500
; Output frequency for energies to log file and energy file =
nstlog                   = 500
nstenergy                = 500
; Output frequency and precision for xtc file =
nstxtcout                = 500
xtc-precision            = 1000


; NEIGHBORSEARCHING PARAMETERS =
cutoff-scheme            = verlet
verlet-buffer-tolerance  = 0.005
nstlist                  = 20
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz

periodic_molecules       = yes
rlist                    = 1.0
nstcalclr                = 10

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = PME
coulomb-modifier         = Potential-shift
rcoulomb-switch          = 0
rcoulomb                 = 0.95
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = PME
vdw-modifier             = Potential-shift
; cut-off lengths        =
rvdw-switch              = 0
rvdw                     = 0.95
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
;fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
;fourier_nx               = 0
;fourier_ny               = 0
;fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = V-rescale
nsttcouple               = 10
; Groups to couple separately =
tc-grps                  = system
;Time constant (ps) and reference temperature (K) =
tau_t                    = 0.1
ref_t                    = 293.15
; Pressure coupling      =
;Pcoupl                   = no
Pcoupl                   = Berendsen
Pcoupltype               = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 1.0
compressibility          = 0 1.6e-8
; compressibility of ionic liquid ... 4.5e-5 for water  1.6e-8 for IL
ref_p                    = 1.0 1.0
nstpcouple               = 10
; SIMULATED ANNEALING CONTROL =
annealing                = no
; Time at which temperature should be zero (ps) =
; zero-temp_time           = 0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529

energygrps               = EMI BF4 GRA C08 C16
;freezegrps               = GRA
;freezedim                = Y Y Y
;energygrp-excl           = GRA GRA GRA C04 C04 C04
refcoord-scaling          = COM




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