[gmx-users] (no subject)
Alex
nedomacho at gmail.com
Wed Aug 9 22:56:14 CEST 2017
I think it is all pretty simple, at least from what you are describe. If
there are sufficient reason to believe that your membrane should be flat
and not jagged, and your box size (supercell size, in the terminology you
probably prefer) is properly set up, simply allow it to relax in vacuum at
a very low temperature. Say, 5-10K? This is prior to solvating, etc.
I've never worked with MnO2, so I just can't say anything more specific,
sorry.
I hope this helps.
Alex
On Wed, Aug 9, 2017 at 12:10 PM, gangotri dey <holyriver6 at gmail.com> wrote:
> Dear Alex and Mark,
>
> Thank you for your kind reply.
>
> To begin with I am a Postdoc but with expertise is in DFT. It is my first
> venture into force field MD calculations. Hence, I am struggling. My group
> and the boss has similar expertise. So we have turned to public forums to
> ask questions.
>
> My system is a brick floating in the water as you have correctly
> identified.
> My system is a periodic MnO2 surface. It has triclinic crystal system. I
> want it to be solvated in all 3 directions but within the boundary of the
> unit cell. This means that I do not want any water molecule between the
> surface and its continuous periodic image. I want the water to be maximum
> in the z-direction. I am using the 5.0.4 version. I tried gmx_mpi
> insert_molecule and then -nmol and -ip option. But this still generates a
> structure with water molecules beyond the desired x and y plane. I am not
> sure how can I get this done as desired.
>
> If the question and the problem are not very clear, please let me know. I
> will try to reframe my words.
>
> Looking forward to a healthy discussion.
>
> Thank you
> G.
>
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> Postdoctoral Associate
> Rutgers University New Brunswick
> Chemistry and Chemical Biology
> 174 Frelinghuysen Road, Piscataway, NJ 08854
> Phone: +16092162254
>
>
>
>
> On Mon, Aug 7, 2017 at 8:06 PM, Alex <nedomacho at gmail.com> wrote:
>
> >
> > I did not quite understand your comment.
> >>>
> >>> However, I am trying my best to answer it.
> >>> I have a surface MnO2 model. I have solvated the structure in all 3
> >>> directions. After that, I minimize it and run NVT simulation with the
> >>> parameters as mentioned. However, I see that there is a deformation of
> >>> the
> >>> surface and it does not remain a flat surface. Instead, it curls like a
> >>> ribbon. This should not be the case. Hence, I am wondering what are the
> >>> factors that can lead to this deformation? Are the parameters in the
> NVT
> >>> simulation good enough or else there is a problem that I cannot see.
> >>>
> >>> G
> >>>
> >>> There are a few points to be made...
> > 1. The shape of your system, which is "solvated in all 3 directions" is
> > very unclear. Is this a brick floating in water?
> > 2. Please do not solvate anything until you have established that your
> > "surface" is happy in vacuum.
> > 3. If you have bending as a whole, it could be indicative of large
> > internal strains, in which case NVT is probably a poor option. When you
> say
> > you have "a surface MnO2 model," is it something like this?
> > https://upload.wikimedia.org/wikipedia/commons/8/81/Manganes
> > e-dioxide-from-xtal-sheet-3D-balls.png
> > 4. This community is mostly focused on biomolecular simulations and noone
> > will be able to verify your parameterization of a solid crystal. Here is
> > the rule of thumb though: If something bends when it shouldn't bend, your
> > model is bad, which really has nothing to do with Gromacs.
> > 5. If you are a student and points 1-4 aren't something your doctoral
> > advisor already mentioned, maybe you should find another advisor.
> >
> > Alex
> >
> >
> > Hi,
> >>>>
> >>>> Are you trying to implement a model that you know is capable of
> produce
> >>>> a
> >>>> surface that does not deform in unexpected ways?
> >>>>
> >>>> Mark
> >>>>
> >>>> On Mon, 7 Aug 2017 16:35 gangotri dey <holyriver6 at gmail.com> wrote:
> >>>>
> >>>> Dear all,
> >>>>>
> >>>>> I am trying to equilibrate a MnO2 surface (not cluster but
> periodic). I
> >>>>> have solvated the surface with water in all 3 directions. After the
> NVT
> >>>>> run, I see that the surface is deformed. I was wondering what else
> can
> >>>>>
> >>>> I
> >>>
> >>>> add in my nvt.mdp to not encounter this problem?
> >>>>>
> >>>>> I have mainly followed the examples in the forum for graphene/CNT
> >>>>>
> >>>> growth.
> >>>
> >>>> title = MnO2 in H2O NVT equilibration
> >>>>> ; Run parameters
> >>>>> integrator = md ; leap-frog integrator
> >>>>> nsteps = 50000 ; 2 * 500000 = 100 ps
> >>>>> dt = 0.002 ; 2 fs
> >>>>> ; Output control
> >>>>> nstxout = 50 ; save coordinates every 0.10 ps
> >>>>> nstvout = 50 ; save velocities every 0.10 ps
> >>>>> nstenergy = 50 ; save energies every 0.10 ps
> >>>>> nstlog = 50 ; update log file every 0.10 ps
> >>>>> ; Bond parameters
> >>>>> continuation = no ; first dynamics run
> >>>>> constraint_algorithm = lincs ; holonomic constraints
> >>>>> constraints = none ; all bonds (even heavy
> atom-H
> >>>>> bonds) constrained
> >>>>> lincs_iter = 1 ; accuracy of LINCS
> >>>>> lincs_order = 4 ; also related to
> accuracy
> >>>>> ; Neighborsearching
> >>>>> cutoff-scheme = Verlet
> >>>>> ns_type = grid ; search neighboring grid
> cells
> >>>>> nstlist = 10 ; 20 fs, largely irrelevant
> >>>>>
> >>>> with
> >>>
> >>>> Verlet
> >>>>> rcoulomb = 1.0 ; short-range electrostatic
> >>>>>
> >>>> cutoff
> >>>>
> >>>>> (in nm)
> >>>>> rvdw = 1.0 ; short-range van der Waals
> >>>>>
> >>>> cutoff
> >>>>
> >>>>> (in nm)
> >>>>> ; Electrostatics
> >>>>> coulombtype = PME ; Particle Mesh Ewald for long-range
> >>>>> electrostatics
> >>>>> pme_order = 4 ; cubic interpolation
> >>>>> fourierspacing = 0.16 ; grid spacing for FFT
> >>>>> ; Temperature coupling is on
> >>>>> tcoupl = V-rescale ; modified Berendsen
> >>>>>
> >>>> thermostat
> >>>>
> >>>>> tc-grps = SOL MnO ; three coupling groups - more accurate
> >>>>> tau_t = 0.1 0.1 ; time constant, in ps
> >>>>> ref_t = 300 300 ; reference temperature, one for
> >>>>>
> >>>> each
> >>>>
> >>>>> group, in K
> >>>>> ; Pressure coupling is off
> >>>>> pcoupl = no ; no pressure coupling in NVT
> >>>>> ; Periodic boundary conditions
> >>>>> pbc = xyz ; 3-D PBC
> >>>>> periodic-molecules = yes
> >>>>> ; Dispersion correction
> >>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
> >>>>> ; Velocity generation
> >>>>> gen_vel = yes ; assign velocities from Maxwell
> >>>>> distribution
> >>>>> gen_temp = 300 ; temperature for Maxwell
> distribution
> >>>>> gen_seed = 188888 ; generate a random seed
> >>>>>
> >>>>>
> >>>>> *Thank you*
> >>>>>
> >>>>> *Gangotri Dey*
> >>>>> Postdoctoral Associate
> >>>>> Rutgers University New Brunswick
> >>>>> Chemistry and Chemical Biology
> >>>>> 174 Frelinghuysen Road, Piscataway, NJ 08854
> >>>>> Phone: +16092162254
> >>>>> --
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