[gmx-users] CNT with BN co doping

[akari karin]

thanks Dr. Vitaly V. Chaban for your reply.

i already simulated the CNT without doping and i have developed a structure
with the doped CNT.

now if i add the dopant atoms in my forcefield file (for example, in my
case i add nonbonded parameters to my ffnonbond.itp and bonded parameters
to my bonded.itp and so on) will it be the correct way to do the simulation?

and it would be very nice if you could explain the statement,

"You must account for the effect of your new fragments on electron density
of the entire nanostructure."

a little bit further.

thanks for your time




On Mon, Jun 30, 2014 at 4:01 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
wrote:

> Simulation of doped nanostructures is much more complicated than
> described below. You must account for the effect of your new fragments
> on electron density of the entire nanostructure. There is enough
> evidence that an additive approach fails here.
>
> Good luck.
>
> Dr. Vitaly V. Chaban
>
>
> On Mon, Jun 30, 2014 at 11:45 AM, akari karin <j.akarikarin at gmail.com>
> wrote:
> > I am trying to simulate carbon nanotubes with some doping. The way i am
> > doping my nanotube is by B-N codoping.
> >
> > i generated the structure but stuck with the topology. i know i need to
> > have the bonded and nonbonded interaction parameters for Boron and
> Nitrogen
> > to do the work but i dont understand how i can get those.
> >
> > i am using the modified oplsaa force field for the simulation of CNT
> > structure. will the default parameters in the oplsaa be okay for my
> > simulation? if not how can i get the parameters?
> >
> > thanks in advance
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