[gmx-users] Infinite system PBC and Bonded Interaction
fileti at ufabc.edu.br
Sat Apr 26 16:10:31 CEST 2008
Now I'm getting a different error.
Suddenly, a water molecule fragments itself and the simulation stops.
And when I do a complete simulation (with a number of steps immediately
before the crash)
it presents many inconsistent shifts. I search the forum for a solution and
the tips were always
to update the Gromacs. I am using version 3.3.3 and errors still occur.
Someone would have any suggestions?
On Fri, Apr 25, 2008 at 10:31 AM, Eudes Fileti <fileti at ufabc.edu.br> wrote:
> 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!
> Thanks again
> > 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 -
> > http://wiki.gromacs.org/index.php/Carbon_Nanotube
> > Mark
> 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
> skype: eefileti
> http://cromo.ufabc.edu.br/~fileti/ <http://cromo.ufabc.edu.br/%7Efileti/>
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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