[gmx-users] Carbon Nanotube Simulations

[George Abadir]

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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