[gmx-users] infinite surface

jimkress_58 jimkress_58 at kressworks.org
Wed Jul 29 16:40:46 CEST 2009


Regarding tutorials and tubes.  Is/ are their any tutorials that describe
how to form a tube, and then add a molecular system within the tube that
flows in one end and out the other, continuously?



-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: Wednesday, July 29, 2009 7:51 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] infinite surface

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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