[gmx-users] Zinc Oxide Simulation
sapnauser365 at gmail.com
Sun Apr 23 06:34:24 CEST 2017
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:
[ 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.
Sapna Mayuri Borah
c/o Dr. A. N. Jha
On Thu, Apr 20, 2017 at 9:29 PM, André Farias de Moura <moura at ufscar.br>
> 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:
> On Thu, Apr 20, 2017 at 9:32 AM, SAPNA BORAH <sapnauser365 at gmail.com>
> > 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
> > 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
> > The simulations have been run without any errors. However, we are
> > 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
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