[gmx-users] Need help creating md.mdp for silica(quartz)?

[Dallas Warren]

1/ it means that between the original coordinate file loaded with vmd and
the frame you are looking at there from the trajectory file, those atoms
have moved across the periodic boundary and vmd is still drawing the bond
between them. vmd knows nothing about bonds, it guesses where the bonds
should be and maintains them between those atoms when viewing a trajectory.
If looking to make a nice looking animation simply using gmx trjconv to
move the layer into the center of the box. Otherwise use a viewing method
in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
each frame i.e. DynamicBonds

2/ where the simulation box is located is entirely arbitrary. So if it is
not in the location you want then use gmx trjconv to move it to where you
want it to be.

All these things you are seeing here are artifacts of the periodic boundary
condition:
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc


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 Mon, 4 May 2020 at 22:08, Ekatherina O <oeg at isc-ras.ru> wrote:

> I have done simulation water in nanopore based on quartz (I use model
> ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is
> a link to the pictures at the initial time (1.png) and in the modeling
> process.
>
> https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing
> )
> Its NVT simulation (see .mdp below) and neutral charge on surface (have
> silanol groups), system is overall neutral.
> 1) Did I choose the right settings?  What do these atomic displacements
> (lines in the pictures) mean? What restrictions should be imposed on the
> system?
> 2) In addition, I noticed that all the atoms of the quartz walls that
> are in the vicinity of the box walls move from the upper wall to the
> lower and lower to the upper. How can I avoid this when periodic
> boundary conditions are imposed? Do I understand correctly that this
> involves interaction between the quartz walls?
>
> integrator          =  md-vv
> dt                  =  0.001            ; = 1 fs
> nsteps              =  500000           ; = 100  ps
> nstcomm             =  1
> ; OUTPUT CONTROL OPTIONS
> nstxout             =  200
> nstvout             =  200
> nstfout             =  200
> nstlog              =  200
> nstenergy           =  200
> energygrps          =  System
> cutoff-scheme            = Verlet
> ; NEIGHBORSEARCHING PARAMETERS
> ;periodic-molecules  =  no
> nstlist             =  20
> ns_type             =  grid
> pbc                 =  xyz
> rlist               =  1.4
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype         =  PME      ; fourierspacing ; pme-order
> ;                   =  PPPM     ; fourierspacing
> ;                   =  Ewald    ; No parallel Ewald.
> rcoulomb            =  1.4
> rvdw                =  1.4
> ; Ewald, PME, PPPM options
> ;fourierspacing      =  0.12
> ;fourier_nx          =  0       ; 2 3 5 7
> ;fourier_ny     =       0
> ;fourier_nz     =       0
> ;pme_order          =  6        ; 10 ; 8 ; default = 4
> optimize_fft        =  yes
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> Tcoupl              =  nose-hoover
> tc-grps             =  System
> tau_t               =  0.5
> ref_t               =  298
> ;Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.1
> compressibility     = 0.0008076
> ref_p               = 800
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel             =  yes
> gen_temp            =  298
> gen_seed            =  173529
> ; OPTIONS FOR BONDS
> constraints         =  all-bonds
> constraint-algorithm     = lincs
>
>
> And sorry if I missed similar topic in mailing list, but I couldn't find
> anything similar.
>
>
> --
> Yours sincerely,
> Ekatherina O.
> oeg at isc-ras.ru
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