[gmx-users] dihedral angles in CNT

Alex nedomacho at gmail.com
Mon Jul 10 12:29:26 CEST 2017

x2top does indeed do that with graphene and CNTs. Strictly speaking, the 
remaining 3/4 of the dihedrals are not redundant, so ideally you should 
test the mechanical properties of your CNT. If the constant for the 
dihedral energy term came from a model, which counts all four dihedrals, 
I would at least try multiplying it by four in your ffbonded file.


On 7/10/2017 2:39 AM, Zuzana Benkova wrote:
> Dear GROMACS users,
> I have used the x2top to generate a topology file for the zig-zag carbon nanotube (6,0). The pbc were applied. I noticed that the number of generated dihedral angles is just a quarter of the total number of the dihedral angles in the CNT. Actually, there are four dihedrals around each bond in CNT but only one is always considered. I just want to be sure if such a reduction is correct. On my opinion this reduction does not affect the definition of the conformation of the CNT since the remaining 3/4 of dihedrals are redundant but is it correct from the viewpoint of dynamics of the system?
> I would appreciate any answer.
> Greetings
> Zuzana

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