[gmx-users] Carbon Nanotube Simulation Issues

Robert Johnson bobjohnson1981 at gmail.com
Tue Jul 24 21:15:01 CEST 2007

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,

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