[gmx-users] Fwd: Ionic liquid and CNTs
candy.a.deck at gmail.com
Thu Jun 28 09:30:48 CEST 2018
Thanks for your answer ...
Here is the pdb file of my system : https://files.fm/u/7crt2yd5
2018-06-27 22:30 GMT+02:00 Alex <nedomacho at 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.
> On Wed, Jun 27, 2018 at 3:47 AM, Candy Deck <candy.a.deck at gmail.com>
> > 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
> > 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
> > 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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