Dear Mark, thank you for your reply and suggestion.<br>I was forgetting the follow detail: <br> " Be absolutely sure that the "terminal" carbon atoms are sharing a bond in the topology file" <br> Now everything is working perfectly!<br>
Thanks again<br>eef<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Message: 1<br>
Date: Fri, 25 Apr 2008 09:14:00 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Infinite system PBC and Bonded Interaction<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:48111438.1020704@anu.edu.au">48111438.1020704@anu.edu.au</a>><br>
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<br>
Eudes Fileti wrote:<br>
> I am simulating a infinite graphene sheet in water.<br>
> The expected is that the system it is infinite in xy plane.<br>
> But after the simulation I note that the edges of the box (in particular<br>
> the graphene) are not replicables, i. e., it do not match with its<br>
> images. I suspect that I may be wrong in using any option mdp file<br>
> I got the same result for both full and xyz for option pbd.<br>
><br>
> What have I to do to my system be infinitely replicated,<br>
> with all its bonded interaction matching?<br>
<br>
There's some advice here for an analogous problem that might help -<br>
<a href="http://wiki.gromacs.org/index.php/Carbon_Nanotube" target="_blank">http://wiki.gromacs.org/index.php/Carbon_Nanotube</a><br>
<br>
Mark<br>
<br>
<br><br></blockquote></div><br>_______________________________________<br>Eudes Eterno Fileti<br>Centro de Ciência Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Catequese, 242 - 3º Andar<br>09090-400 Santo André - SP Brasil<br>
Tel: +55 11 4437-1600 ramal 408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a>