[gmx-users] g_dipoles, take the normal of the computational box

Emanuel Peter Emanuel.Peter at chemie.uni-regensburg.de
Fri Jun 4 09:45:12 CEST 2010

Dear Gromacs users,

I have following question which regards to the g_dipoles tool.
In order to get information about the total dipole moment of my protein I wrote following command:

g_dipoles -f  *.trr -s *.tpr -n *.ndx -o Mtot.xvg -a average.xvg 

When I looked at the default options, the Z-axis is chosen to be the normal of the computational box.
This is defined by the option -axis.
I changed that option in order to test to the Y-axis and obtained a totally different result for my total 
dipole moment. But as far as I know the total dipole moment should not depend on any axis. Could
you tell me what this normal-vector(?) means?
Isn't the total dipole moment defined as: mu_tot = (mu_x^2 + mu_y^2 +  mu_z^2)^(1/2) ?
What is the normal of the computational box good for?

Thank you in advance for your kind answer.

Best regards,

Emanuel Peter

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