[gmx-users] MnO2 periodic system

[Dallas Warren]

What do you mean "deformed"?

The "deformation" that you have encountered is probably most likely
due to the topology, rather than the simulation settings (since you
have constant volume set).  So that means there are issues with your
topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 5 August 2017 at 02:51, gangotri dey <holyriver6 at gmail.com> wrote:
> Dear all,
>
> I am trying to equilibrate a MnO2 surface (not cluster periodic). 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*
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