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

[Elie M]

 I will have a look at the suggested tutorials. Many thanks
Elie

Date: Tue, 17 Apr 2012 23:09:21 -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 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 knowa few of the authors personally. 

you don't really need to get a perfect position.
you can pretty much build the polymer witha simple molecule editor to be a straight chain,move it somewhere in space, merge it with the
CNT structure and a suitably sized pre-equilibratedwater box while removing the overlaps. then carefully relax the structure and equilibrate tothe proper density. this is all pretty straightforward
classical MD protocol for multi-component systems.
using quantum espresso programs onany of this will just be a massive wasteof time. i strongly suggest you pick a
more suitable forum to get advice, and looks at tutorials, e.g. for proteins embeddedin 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.
 		 	   		  
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