[gmx-users] Carbon Nanotube Simulations
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
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,
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.
> On 3/27/07, George Abadir <georgea at ece.ubc.ca> wrote:
>> 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
>> I get a warning that "all CONECT records are ignored" but there is no
>> Second, I don't know exactly what the next step to perform an MD
>> 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
>> 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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