[gmx-users] (no subject)

[gangotri dey]

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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