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

[David van der Spoel]

On 2010-06-04 09.45, Emanuel Peter wrote:
> 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
>
>
>
The axis is used only for computing the dipole per slice of the box. Not 
sure how this can affect the total dipole though. Please file a bugzilla 
with a short example.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se