[gmx-users] Fwd: Ionic liquid and CNTs
Alex
nedomacho at gmail.com
Thu Jun 28 09:43:05 CEST 2018
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 <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.
>>
>> 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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