[gmx-users] Re: Re: Normal of the benzene and z axis.

[Eudes Fileti]

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 <fileti at ufabc.edu.br>
> Subject: [gmx-users] Re: Normal of the benzene and z axis.
> To: gmx-users at gromacs.org
> Message-ID:
>        <65e289a20906030508y708e2633rddba6dc6c8f1642a at mail.gmail.com>
> 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 <fileti at ufabc.edu.br> 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
> >
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> ------------------------------
>
> 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 <fileti at ufabc.edu.br
> > <mailto:fileti at ufabc.edu.br>> 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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