[gmx-users] infinite surface

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 29 13:50:37 CEST 2009

Giulio Scocchi wrote:
> Hello everybody.
> I am a Gromacs beginner, so sorry if this question is trivial and/or I
> am not precise. I would like to simulate an infinite surface of graphene
> (or any other planar lattice structure). Gromacs supports pbc also in
> two directions (as far as I understood) and that would really be perfect
> for my purposes but.. in order to have a periodic infinite lattice, I
> need to have atoms on one face of the cell being connected to the atoms
> on the opposite face. So, how can I do this? Just by modifying the
> CONNECT section of the input .pdb file? Will gmx programs understand? J

No, GROMACS ignores CONNECT sections. Check out the advice here. 


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