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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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