[gmx-users] Zinc Oxide Simulation

[Justin Lemkul]

On 4/23/17 12:34 AM, SAPNA BORAH wrote:
> Dear Andre,
>
> Thanks for the suggestions.
>
> For the charges, we had also taken a reference from another simulation
> performed for ZnO nanowires in gromacs. Following is the information:
>
> [ ZnO]
>  [ atoms ]
>    ZN   ZN      2.000       0
>    O    O      -0.040       0
>    OS   OS    -2.040      0
> [ bonds ]
>  [ angles ]
> ;  ai    aj    ak   gromos type
>  [ impropers ]
> ;  ai    aj    ak    al   gromos type
>  [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>
>
> Where, the OS is the shell oxygen.
>
> However when run for ZnO nanoparticles, the energy minimisation stops with
> a segmentation fault error.
>
> When replaced with the charges mentioned in the previous mail, the
> simulation runs, which makes it altogether more doubtful.
>
> Nonetheless, I am still trying and hoping for a few suggestions here to get
> hold of some fair ZnO parameters.
>

If you're using a "shell oxygen," that implies a polarizable simulation, which 
is set up differently.  If you're just specifying three normal atoms with no 
bonded interactions (a shell particle and its parent nucleus are connected) then 
your model simply isn't realistic.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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