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

[David van der Spoel]

Eudes Fileti wrote:
> 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? 

g_sorient -h:

g_sorient analyzes solvent orientation around solutes. It calculates two
angles between the vector from one or more reference positions to the first
atom of each solvent molecule:
theta1: the angle with the vector from the first atom of the solvent 
molecule
to the midpoint between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the same
three atoms, or when the option -v23 is set the angle with the vector 
between
atoms 2 and 3.
The reference can be a set of atoms or the center of mass of a set of atoms.
The group of solvent atoms should consist of 3 atoms per solvent molecule.
Only solvent molecules between -rmin and -rmax are considered for -o and -no
each frame.



> 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 <mailto:fileti at ufabc.edu.br>>
>     Subject: [gmx-users] Re: Normal of the benzene and z axis.
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID:
>            <65e289a20906030508y708e2633rddba6dc6c8f1642a at mail.gmail.com
>     <mailto: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
>     <mailto: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>
>      > <mailto: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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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