[gmx-users] Infinite system PBC and Bonded Interaction
fileti at ufabc.edu.br
Fri Apr 25 15:31:23 CEST 2008
Dear Mark, thank you for your reply and suggestion.
I was forgetting the follow detail:
" Be absolutely sure that the "terminal" carbon atoms are sharing a bond in
the topology file"
Now everything is working perfectly!
> Message: 1
> Date: Fri, 25 Apr 2008 09:14:00 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Infinite system PBC and Bonded Interaction
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <48111438.1020704 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Eudes Fileti wrote:
> > I am simulating a infinite graphene sheet in water.
> > The expected is that the system it is infinite in xy plane.
> > But after the simulation I note that the edges of the box (in particular
> > the graphene) are not replicables, i. e., it do not match with its
> > images. I suspect that I may be wrong in using any option mdp file
> > I got the same result for both full and xyz for option pbd.
> > What have I to do to my system be infinitely replicated,
> > with all its bonded interaction matching?
> There's some advice here for an analogous problem that might help -
Eudes Eterno Fileti
Centro de Ciência Naturais e Humanas
Universidade Federal do ABC
Rua Catequese, 242 - 3º Andar
09090-400 Santo André - SP Brasil
Tel: +55 11 4437-1600 ramal 408
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