Dear gromacs user, I am doing the MD simulation of CNT-DNA interaction. Before introducing DNA, I used gromacs default force field and finished the simulation of CNT (carbon nanotube). And, in the ffgmxnb.itp, I introduced the non-bonded parameters for C-C and C-OW (oxygen) in the [non-bonded param] session.
Now, I have the amber99 package. I opened ffamber99nb.itp and compared the format of ffamber99nb.itp to ffgmxnb.itp. There is only [atoms] session in ffamber99nb.itp. Do you mind telling me how to introduce these non-bonded parameters (L-J parameters) for C-C and C-OW in ffamber? Do I just simply add [non-bonded param] at the end of the ffamber99nb.itp and list the parameters there? I guess this is important for me because I attempted to add [non-bonded param] at the end of the itp file. After the energy minimization, I visualized that the carbon nanotube is standing above the simulation box. Also, I realize that the atom mass in ffamberXX.itp is 0, but in ffamberXX.atp, all masses are non-zero. Do you minding explain it for me in detail? I appreciate your help. Regards! Bo
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