[gmx-users] Carbon Nanotube Simulations

George Abadir georgea at ece.ubc.ca
Thu Mar 29 02:13:01 CEST 2007


Thank you very much for your reply.
I have added a couple of lines in the ffgmx.n2t file :" C    C    1     
C (for the C atom with 1 bond)
                                                                               
C    C   2     C       C  (for the C atom with 2 bonds)
I also changed the ffgmxbon.itp file, adding a line under [bondtypes] 
:"C        C        1        0.14210      478900"
I also changed the parameters for the angles. Still I get the same error 
that "No forcefield type for atom C(1) with 1 bonds".
Also, the Morse potential has a parameter gamma that I don't know where 
it can be defined, I can see that only the reference bond length (b0) 
and the stretch force constant (kb) can be defined, so how can I define 
gamma?
If somebody did make these changes before I would be very thankful if he 
would send me the modified files or advise me of how to do it.
Thank you very much for your help,
George

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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