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I will have a look at the suggested tutorials. Many thanks<div><br></div><div>Elie<br><br><div><div id="SkyDrivePlaceholder"></div><hr id="stopSpelling">Date: Tue, 17 Apr 2012 23:09:21 -0400<br>Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube attached to a polymer<br>From: akohlmey@gmail.com<br>To: elie.moujaes@hotmail.co.uk<br>CC: pw_forum@pwscf.org<br><br><br><br><div class="ecxgmail_quote">On Tue, Apr 17, 2012 at 10:50 PM, Elie M <span dir="ltr"><<a href="mailto:elie.moujaes@hotmail.co.uk">elie.moujaes@hotmail.co.uk</a>></span> wrote:<br><blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex">
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Hello,<div><br></div><div>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..</div>
</div></div></blockquote><div><br></div><div>well, again, this is *definitely* the wrong forum.</div><div>the paper is about classical MD. i actually know</div><div>a few of the authors personally. </div><div><br></div><div>
you don't really need to get a perfect position.</div><div><br></div><div>you can pretty much build the polymer with</div><div>a simple molecule editor to be a straight chain,</div><div>move it somewhere in space, merge it with the</div>
<div>CNT structure and a suitably sized pre-equilibrated</div><div>water box while removing the overlaps. then </div><div>carefully relax the structure and equilibrate to</div><div>the proper density. this is all pretty straightforward</div>
<div>classical MD protocol for multi-component systems.</div><div><br></div><div>using quantum espresso programs on</div><div>any of this will just be a massive waste</div><div>of time. i strongly suggest you pick a</div>
<div>more suitable forum to get advice, and </div><div>looks at tutorials, e.g. for proteins embedded</div><div>in lipid bilayers (which require a similar </div><div>setup and equilibration protocol).</div><div><br></div>
<div>axel.</div><div><br></div><div><br></div><blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex"><div><div dir="ltr"><div><br></div><div><br></div><div>Regards</div><div>
<br></div><div>Elie<br><br><div><div></div>> Date: Tue, 17 Apr 2012 11:31:15 -0400<br>> Subject: Re: [Pw_forum] forming a supercell for a (10, 0) nanotube attached to a polymer<br>> From: <a href="mailto:akohlmey@gmail.com">akohlmey@gmail.com</a><br>
> To: <a href="mailto:elie.moujaes@hotmail.co.uk">elie.moujaes@hotmail.co.uk</a><br>> CC: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><div><div class="h5"><br>> <br>> On Tue, Apr 17, 2012 at 11:19 AM, Elie M <<a href="mailto:elie.moujaes@hotmail.co.uk">elie.moujaes@hotmail.co.uk</a>> wrote:<br>
> > Dear all,<br>> ><br>> > I am trying to study the dynamics of a (10,0) nanotube attached to a<br>> > polymer. Does anyone know of any code that forms supercells for such<br>> > systems? Any examples on that?<br>
> <br>> are you sure you are posting to the right forum?<br>> as a q-e calculation, this would likely be very demanding.<br>> <br>> what kind of polymer and how much of it?<br>> <br>> i've written some plugins for VMD that can<br>
> combine coordinate files and remove overlap.<br>> there also is a plugin that can generate a<br>> (10,0)-SWCNT. also, i don't think you want<br>> to start a q-e calculation on this right away,<br>> but do a good equilibration with a classical<br>
> model first, or else you'd be wasting a serious<br>> amount of CPU time.<br>> <br>> axel.<br>> <br>> ><br>> > Thanks<br>> ><br>> > Regards<br>> ><br>> > Elie Moujaes<br>
> > University of Notts<br>> > NG7 2RD<br>> > Notts<br>> > UK<br>> ><br>> > _______________________________________________<br>> > Pw_forum mailing list<br>> > <a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
> > <a href="http://www.democritos.it/mailman/listinfo/pw_forum" target="_blank">http://www.democritos.it/mailman/listinfo/pw_forum</a><br>> ><br>> <br>> <br>> <br>> -- <br>> Dr. Axel Kohlmeyer<br>
> <a href="mailto:akohlmey@gmail.com">akohlmey@gmail.com</a> <a href="http://goo.gl/1wk0" target="_blank">http://goo.gl/1wk0</a><br>> <br>> College of Science and Technology<br>> Temple University, Philadelphia PA, USA.<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Dr. Axel Kohlmeyer <br><a href="mailto:akohlmey@gmail.com">akohlmey@gmail.com</a> <a href="http://goo.gl/1wk0" target="_blank">http://goo.gl/1wk0</a><br>
<br>College of Science and Technology<br>Temple University, Philadelphia PA, USA.<br></div></div> </div></body>
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