[gmx-users] Graphene sheet topology

[Alex]

Did you try googling "gromacs graphene topology" or "gromacs cnt 
topology"? To refine the interactions in existing tutorials, I actually 
wrote a paper a while back: 
http://iopscience.iop.org/article/10.1088/0957-4484/25/48/485701/meta -- 
which noone seems to cite. :)

Improper dihedrals are generated automatically by programs like x2top, 
but whether they are necessary actually depends on how you build the 
graphene model, including how many dihedrals per C-C bond. If you run 
x2top with -alldih, all dihedrals will be converted to proper dihedrals.

Alex


On 3/17/2018 12:30 PM, Mostafa Fakhraee wrote:
> Hi,
>
> Does anyone know how to build a graphene topology based on OPLS-AA force
> field?
>
> Also is it possible to let me know how can I determine the improper
> dihedral of graphene because graphene sheet has a lot of dihedrals and it
> is difficult for do that manually?
>