[gmx-users] Zinc Oxide Simulation

[SAPNA BORAH]

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.

Thanks.

Sapna.



Sapna Mayuri Borah
c/o Dr. A. N. Jha
Research student
Tezpur University,
India

On Thu, Apr 20, 2017 at 9:29 PM, André Farias de Moura <moura at ufscar.br>
wrote:

> Hi Sapna,
>
> just a few general comments:
>
> (1) mixing parameters from different force fields is nearly always a bad
> idea. In your case, it is probably worse, since Mulliken charges are not
> actual force field charges.
>
> (2) as a matter of fact, any charges from the reference you have pick up
> should be seen with caution, since they report either DFT calculations or
> ReaxFF simulations (which is not supported by GROMACS)
>
> (3) any Zn2+ or O parameters from GROMOS or other force fields available
> within GROMACS are not meant to treat ZnO or other similar material, they
> usually apply to single zinc ions and small molecules containing oxygen.
>
> (4) there are classical nonreactive force fields available, but you need to
> check if they can reproduce the phases you're interested in. For instance:
> http://pubs.acs.org/doi/full/10.1021/la9022739
>
> best
>
> Andre
>
>
>
> On Thu, Apr 20, 2017 at 9:32 AM, SAPNA BORAH <sapnauser365 at gmail.com>
> wrote:
>
> > Hi!
> >
> > We are working with ZnO nanoparticle structures generated from Virtual
> > NanoLab Software, using the Wulff constructor.
> >
> > We are using gromos54a7ff for the simulation, and introduced ZnO
> parameters
> > from literature.
> > Partial charges for Zn= 1.026. For O= -1.026.
> > (Surface Science 602 (2008) 1020–1031)
> >
> > Apart from this, the gromosff has default non bonded parameters for Zn2+
> > and O.
> >
> > No information of ZnO bonded has been included, considering it to be
> ionic.
> >
> > The simulations have been run without any errors. However, we are
> doubtful
> > about the charges and the usage of Zn2+.
> >
> > Any suggestion regarding this procedure would be appreciated. Thanks in
> > advance.
> >
> > Sapna.
> > Cheers.
> >
> >
> > Sapna Mayuri Borah
> > c/o Dr. A. N. Jha
> > Research student
> > Tezpur University,
> > India
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> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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