From: "Eudes Fileti" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@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.
Berk.
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