[gmx-users] (no subject)

[Mark Abraham]

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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