Dear David, thanks for the reply. In fact 3 carbons can provide me the normal vector of the molecule. But according to manual, g_sorient considers the angle formed by the triple 1 2 3, as the vector that goes from 2 to the midpoint of 1 and 3 (which is the plan of the molecule). So how can I to build a index file for g_sorient to plot the normal vector? Sorry if the question is obvious and I can't to see. Bests _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4437-0196 > > > ---------------------------- > > Message: 5 > Date: Wed, 3 Jun 2009 09:08:43 -0300 > From: Eudes Fileti <[email protected]> > Subject: [gmx-users] Re: Normal of the benzene and z axis. > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="windows-1252" > > Thanks for the reply. > But I have tried use g_sorient tool and I could > not see what the sequence of index give me a normal > vector of the molecule of benzene. > There another tool for this analysis? > Bests > eef > _______________________________________ > Eudes Eterno Fileti > Centro de Ciências Naturais e Humanas > Universidade Federal do ABC — CCNH > Av. dos Estados, 5001 > Santo André - SP - Brasil > CEP 09210-971 > +55.11.4437-0196 > http://fileti.ufabc.edu.br > > > On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti <[email protected]> wrote: > > > Dear gmx users;How can I calculate the angle distribution forthe angle > > between the normal of the benzene and z axis? > > Bests > > eef > > _______________________________________ > > Eudes Eterno Fileti > > Centro de Ciências Naturais e Humanas > > Universidade Federal do ABC — CCNH > > Av. dos Estados, 5001 > > Santo André - SP - Brasil > > CEP 09210-971 > > +55.11.4437-0196 > > http://fileti.ufabc.edu.br > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090603/31b76231/attachment-0001.html > > ------------------------------ > > Eudes Fileti wrote: > > Thanks for the reply. > > But I have tried use g_sorient tool and I could > > not see what the sequence of index give me a normal > > vector of the molecule of benzene. > three carbons in the ring. > > There another tool for this analysis? > > Bests > > eef > > _______________________________________ > > Eudes Eterno Fileti > > Centro de Ciências Naturais e Humanas > > Universidade Federal do ABC — CCNH > > Av. dos Estados, 5001 > > Santo André - SP - Brasil > > CEP 09210-971 > > +55.11.4437-0196 > > http://fileti.ufabc.edu.br > > > > > > On Tue, Jun 2, 2009 at 9:01 AM, Eudes Fileti <[email protected] > > <mailto:[email protected]>> wrote: > > > > Dear gmx users; > > How can I calculate the angle distribution for > > the angle between the normal of the benzene and z axis? > > Bests > > eef > > _______________________________________ > > Eudes Eterno Fileti > > Centro de Ciências Naturais e Humanas > > Universidade Federal do ABC — CCNH > > Av. dos Estados, 5001 > > Santo André - SP - Brasil > > CEP 09210-971 > > +55.11.4437-0196 > > http://fileti.ufabc.edu.br > > > >
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