[gmx-users] g_sorient. Again.

Berk Hess gmx3 at hotmail.com
Wed Jan 31 10:05:24 CET 2007

>From: "Eudes Fileti" <fileti at ufabc.edu.br>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] g_sorient. Again.
>Date: Tue, 30 Jan 2007 22:57:45 -0200
>Dear Berk,
>Thank you for the reply.
>Actually my problem is not related to the analysis of bonds
>but of angles. Specifically, I am interested in the distribution
>of the angle I between the C=C bond of etanol with a plan of
>my solute molecule. It also would be interesting to analyze
>as this angle varies with the distance, since I believe that
>solute modifies significantly the local structure of the solvent.
>Could you suggest me a procedure or tool?

My suggestion is exactly for the angles.
If the first C is atom 1 and the second atom 2, then an index
group of 1 2 2 results in the "dipole" in g_sorient being the C=C
vector. You can then analyze bond orientations by looking
at the "dipole" angles.


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