Ah, that's a scary looking system. :)
Indeed, there are vacuum pockets, because the system has not been
brought to correct pressure. All you have to do for your relaxation run
is use a semiisotropic barostat (maybe Berendsen, but only for
relaxation) with a realistic solvent compressibility in the Z-direction
and zero compressibility in the XY-plane. Gromacs allows this rather
easily. And run it for something like 5-10 ns, not 0.5 ns.
Alex
On 6/28/2018 1:30 AM, Candy Deck wrote:
Hi Alex,
Thanks for your answer ...
Here is the pdb file of my system : https://files.fm/u/7crt2yd5
Candy
2018-06-27 22:30 GMT+02:00 Alex <nedoma...@gmail.com>:
If there is a bubble, all it could mean is that the volume simply too
large, which could be expected, given the combination of short simulation
and low compressibility. It is also unclear what your system looks like.
Please upload your pdb or an image somewhere.
Alex
On Wed, Jun 27, 2018 at 3:47 AM, Candy Deck <candy.a.d...@gmail.com>
wrote:
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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