# [gmx-users] Instantaneous dipole moment of water molecule

Deepak Ojha alwaysinthemind at gmail.com
Wed Sep 12 08:56:16 CEST 2012

```Dear All

I want to calculate instantaneous dipole moment of a water
molecule(from liquid water) in gromacs.I had gone through the archives
of the forum but couldn't found much.

I used command g_dipoles with following extension
g_dipoles -f 293.trr -s 293.tpr -n atoms.ndx  -o Mtot.xvg  -mu -1

atoms.ndx contains three atoms of a water molecule.

which gave the output as
Dipole moment (Debye)
---------------------
Average  =   2.2740  Std. Dev. =   0.0007  Error =   0.0000

The following averages for the complete trajectory have been calculated:

Total < M_x > = -0.00546922 Debye
Total < M_y > = 0.0192573 Debye
Total < M_z > = -0.0446763 Debye

Total < M_x^2 > = 1.68877 Debye^2
Total < M_y^2 > = 1.71468 Debye^2
Total < M_z^2 > = 1.76741 Debye^2

Total < |M|^2 > = 5.17086 Debye^2
Total < |M| >^2 = 0.00239673 Debye^2

< |M|^2 > - < |M| >^2 = 5.16846 Debye^2

Finite system Kirkwood g factor G_k = 0.999537
Infinite system Kirkwood g factor g_k = 0.978649

Epsilon = 1.06689

I am convinced with the value in comparison to that reported in literature.
But when I plot the Mtot.xvg I found the fluctuations in dipole from
-2.5 to 2.5 D. Is
it reasonable to have this kind of behaviour or is it due to change in
the direction of
dipole vector. I need instantaneous fluctuations to calculate dipole
correlation function.

Further to calculate dipole moment of water  I believe  I should use
Dflexible in mdp file,for without fluctuations the dipole for rigid
water molecule must not
change .But It has been strongly demotivated in previous