[gmx-users] Fwd: Ionic liquid and CNTs
Candy Deck
candy.a.deck at gmail.com
Thu Jun 28 09:56:38 CEST 2018
Thanks a lot !
I'm going to do it straight away ...
I'll let you know the results !
Thanks ever so much !
Candy
2018-06-28 9:43 GMT+02:00 Alex <nedomacho at gmail.com>:
> 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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