[gmx-users] (no subject)

[Mark Abraham]

Hi,

On the information given, nobody can tell whether the parameters you have
for the interactions between Mn and O and maybe water are unsuitable, or
that something is wrong with the method, or the initial conditions, or the
code.

Mark

On Mon, 7 Aug 2017 23:11 gangotri dey <holyriver6 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
>
>
>
> *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 5:04 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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