[gmx-users] CNT with BN co doping

[Dr. Vitaly Chaban]

I do not believe that your methodological solution is physically relevant

Dr. Vitaly V. Chaban


On Mon, Jun 30, 2014 at 12:33 PM, akari karin <j.akarikarin at gmail.com> wrote:
> 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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