[gmx-users] Carbon Nanotube Simulations

Robert Johnson bobjohnson1981 at gmail.com
Wed Mar 28 17:13:12 CEST 2007

When using x2top with a specific force field, things are assumed about
the connectivity of the molecule. The terminal carbon atoms of your NT
will only be bonded to, at most, 2 other carbons. In your case, it
looks like they are only bonded to one. When x2top tries to find the
forcefield associated with a carbon bonded to only one other carbon,
you get an error because such information doesn't exist. One option
would be to cap the nanotube with hydrogens. The other would be to add
information about a singly bonded carbon into the force field.

If you want to simulate an infinite nanotube by using periodic
boundary conditions, you have to make certain that a couple criteria
are satisfied. One, you have to make sure your nanotube is actually
periodic (i.e. if you translate it by one lattice constant will all of
the bonds match up?). Second, you have to make sure the nanotube is
oriented correctly in a box of the right dimensions. If your nanotube
is aligned along the z-direction, you have to make sure the Lz box
dimension is commensurate with the periodicity of the nanotube. You
can then generate an "infinite" nanotube with the x2top -pbc option.
Here, x2top will recognize that the terminal C atoms actually share a
chemical bond. Thus, you won't get an error about a single bonded C.

On 3/27/07, George Abadir <georgea at ece.ubc.ca> wrote:
>  Hi,
>       I added CNT residue in the ffgmx.rtp as follows:
>                   " [ CNT ]
>  [ atoms ]
>  C C 0.00 0"
> Then I used x2top to generate the topology for carbon nanotubes from the PDB
> file generated form TUBEGEN. First, if I use any format in TUBEGEN other
> than the PDB with periodic boundary conditions, I get an error "No
> forcefield type for atom C(1) with 1 bonds". When I use the PDB-PBC format,
> I get a warning that "all CONECT records are ignored" but there is no error.
> Second, I don't know exactly what the next step to perform an MD simulation
> just for the CNT alone is? When I use grompp I get an error "the cut-off
> length is longer than the half the shortest box vector or longer than the
> smallest box diagonal element. Increase the box size or decrease rlist". Are
> there any missing steps? I would appreciate if anybody would inform me of
> the necessary steps to do such a simulation (actually my ultimate goal is to
> perform an MD simulation for a CNT-DNA and a CNT-protein system).
> Thank you very much in advance,
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