[gmx-users] Fwd: Ionic liquid and CNTs

[Alex]

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.deck at 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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