Hello all 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? Thanks eef
On Fri, Apr 25, 2008 at 10:31 AM, Eudes Fileti <[EMAIL PROTECTED]> 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 > eef > > > > > Message: 1 > > Date: Fri, 25 Apr 2008 09:14:00 +1000 > > From: Mark Abraham <[EMAIL PROTECTED]> > > Subject: Re: [gmx-users] Infinite system PBC and Bonded Interaction > > To: Discussion list for GROMACS users <[email protected]> > > Message-ID: <[EMAIL PROTECTED]> > > 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 skype: eefileti http://cromo.ufabc.edu.br/~fileti/
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