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 <nedoma...@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 <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 >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at http://www.gromacs.org/ >>>> Support/Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? 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