[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
discussions.Please help me in this regard.

DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others
to live as one wishes to live"

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