I want to set CNT infinite in the system of CNT and water. I'm using GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file.
I set the box size larger than CNT's length a C-C bond(half up and half down).
If I don't do a EM, it will crumble. But if I do it,it can't satisfy that the box size is larger then CN't length a C-C bond.
I have searched google and gmx mail list, but still can't solve it .
I found that GMX online document about Carbon Nanotube(http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube)
say,
Be absolutely sure that the "terminal" carbon atoms are sharing a bond in the topology file.
I don't understand it.How should I do?
Thanks!
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