[gmx-users] Carbon Nanotube Simulations

George Abadir georgea at ece.ubc.ca
Thu Mar 29 04:41:22 CEST 2007

Hi, thank you very much for your help.
I capped the CNT with hydrogen atoms (i.e., I changed the carbon atoms 
at the ends of the tube into hydrogen atoms), but now I get an error "No
forcefield type for atom C(1) with 2 bonds" instead of ""No forcefield 
type for atom C(2) with 1 bonds" ! Is there any way to solve this?
Thank you very much in advance,

Robert Johnson wrote:

> 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.
> Bob
> 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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