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://www.democritos.it/pipermail/pw_forum/attachments/20120417/384f78f8/attachment.htm