[Pw_forum] forming a supercell for a (10, 0) nanotube attached to a polymer

[Axel Kohlmeyer]

On Tue, Apr 17, 2012 at 10:50 PM, Elie M <elie.moujaes at hotmail.co.uk> wrote:

>  Hello,
>
> Thanks for the reply..actually I am trying to reproduce the Molecular
> dynamics obtained in the paper entitled" Helical Wrapping of SWNT by water
> soluble Poly (--phenyleneethynylene) , nano letters, 2009, Vol 9 No 4,
> 1414-1418 where did the MD of 10,0 nanotube with a polymer called PPES. I
> was able to build the 10,0 nantube but have no idea how to attach the
> polymer; in other words how to get the positions of the several atoms in
> the molecule and to attach it to the nanotube to build the supercell which
> will be ready for calculations..This is the software  am looking for..
>

well, again, this is *definitely* the wrong forum.
the paper is about classical MD. i actually know
a few of the authors personally.

you don't really need to get a perfect position.

you can pretty much build the polymer with
a simple molecule editor to be a straight chain,
move it somewhere in space, merge it with the
CNT structure and a suitably sized pre-equilibrated
water box while removing the overlaps. then
carefully relax the structure and equilibrate to
the proper density. this is all pretty straightforward
classical MD protocol for multi-component systems.

using quantum espresso programs on
any of this will just be a massive waste
of time. i strongly suggest you pick a
more suitable forum to get advice, and
looks at tutorials, e.g. for proteins embedded
in lipid bilayers (which require a similar
setup and equilibration protocol).

axel.



>
> Regards
>
> Elie
>
> > Date: Tue, 17 Apr 2012 11:31:15 -0400
> > Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube
> attached to a polymer
> > From: akohlmey at gmail.com
> > To: elie.moujaes at hotmail.co.uk
> > CC: pw_forum at pwscf.org
>
> >
> > On Tue, Apr 17, 2012 at 11:19 AM, Elie M <elie.moujaes at hotmail.co.uk>
> wrote:
> > > Dear all,
> > >
> > > I am trying to study the dynamics of a (10,0) nanotube attached to a
> > > polymer. Does anyone know of any code that forms supercells for such
> > > systems? Any examples on that?
> >
> > are you sure you are posting to the right forum?
> > as a q-e calculation, this would likely be very demanding.
> >
> > what kind of polymer and how much of it?
> >
> > i've written some plugins for VMD that can
> > combine coordinate files and remove overlap.
> > there also is a plugin that can generate a
> > (10,0)-SWCNT. also, i don't think you want
> > to start a q-e calculation on this right away,
> > but do a good equilibration with a classical
> > model first, or else you'd be wasting a serious
> > amount of CPU time.
> >
> > axel.
> >
> > >
> > > Thanks
> > >
> > > Regards
> > >
> > > Elie Moujaes
> > > University of Notts
> > > NG7 2RD
> > > Notts
> > > UK
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey at gmail.com  http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20120417/384f78f8/attachment.html>