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.akarika...@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 <vvcha...@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.akarika...@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 >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >> a mail to gmx-users-requ...@gromacs.org. > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.