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 <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] Re: Normal of the benzene and z axis.
To: [email protected] <mailto:[email protected]>
Message-ID:
<[email protected]
<mailto:[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]
<mailto:[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
>
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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 <[email protected]
<mailto:[email protected]>
> <mailto:[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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--
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
[email protected] [email protected] http://folding.bmc.uu.se
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