[gmx-users] Re: Carbon Nanotube Simulation Issues

Christopher Stiles CS145331 at albany.edu
Tue Jul 24 22:22:04 CEST 2007

Hi Bob,

     Thank you so much for the quick and detailed response. I am looking to
simulate a finite CNT. I do have one point of clarification though, when you
say you will have to add in the force field parameters afterwards, does this
mean I must pick the force field I wish to use after wards and manually put
that in or are your referring to the Residue (in the *.pdb file it is


Thank you again,


~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE)

State University of New York, Albany, New York 12203, USA


> Hi Chris,

> Can you visualize your nanotube coordinates with a program like VMD to

> make sure that it looks ok? However, I'd assume your coordinate file

> is just fine.


> First off, do you want to simulate a finite nanotube or an infinite

> nanotube?


> If you want an infinite nanotube do this:

> 1) Orient nanotube along z-axis (probably this is already done)

> 2) Determine the length L of the nanotube

> 3) Generate a box around your nanotube coordinates with a z-dimension

> equal to L+b. Here, b is the amount of extra space needed to make your

> nanotube to be periodic. Use this command: editconf -f nt-coords.pdb

> -o nt-box.pdb -c -box 10 10 <L+b>

> 4) Generate topology with this comand: x2top -f nt-box.pdb -o

> nt-infinite.top -pbc -ff gmx

> This will generate a topology with definitions for the bonds, angles

> and dihedrals. You will have to edit this file to include the force

> field parameters for each of these interactions. However, since every

> single atom in your nanotube is the same, the interactions all have

> the same parameters.


> If you want a finite nanotube that is capped with hydrogens you should

> use this command:

> x2top -f nt.pdb -o nt.top -ff gmx


> Again, you will have to add in the force field parameters afterwards.

> However, this is trivial since all the interactions are identical.

> Good luck,

> Bob







> On 7/24/07, Christopher Stiles <CS145331 at albany.edu

> <http://www.gromacs.org/mailman/listinfo/gmx-users> > wrote:





>> I am trying to simulate a single wall carbon nanotube in a box solvated

>> in

>> water, at 300k for about 200ps. Also once I accomplish this I wish to

>> fix

>> either one end of the tube or fix the center of mass position, although

> this

>> part is unimportant if I can not get the thing to run at all yet.




>> I have created a page with a full detailed account of what I have done

>> and

>> tried so far. http://cs86.com/CNSE/SWNT.htm


>> Please note all files where created with Vim in the unix environment so

>> I

>> think I have eliminated the formatting issues.


>> Also that I have tried the simulation with many different sized tubes

>> from

>> TubeGen

>> (http://turin.nss.udel.edu/research/tubegenonline.html ),

>> both with and without hydrogen capped ends (this is something I have

>> read

> in

>> the archives as a possible solution, it makes no difference in the end).




>> I have come to the conclusion through the help of many of you that the

> *.pdb

>> file from TubeGen and mainly the residue "UNK" among other things. If

>> any

>> one has had luck with using a TubeGen file to create a simulation please

> let

>> me know as to how. Other wise I am looking at a few new options

>> basically

>> all of them involve writing my own files.




>> I guess I am looking for advice where to go from here.


>>   ~Christopher Stiles

>> College of Nanoscale Science and Engineering (CNSE)

>> State University of New York, Albany, New York 12203, USA

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