[gmx-users] g_dipoles

[rams rams]

Dear Users,

I am trying to obtain the dipole moment of a 40 amino acid residue peptide
using g_dipoles. I am getting a huge number (about 700 Debye). I expect it
to be around 150 Debye (based on other studies). To make sure it I extracted
a shapshot of the structure and obtained the dipolemoment using the
following command:

g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx

I am giving the last few lines of the output below:

Dipole moment (Debye)
---------------------
Average  = 516.7213  Std. Dev. =   0.0000  Error =   0.0000

The following averages for the complete trajectory have been calculated:

 Total < M_x > = -54.3459 Debye
 Total < M_y > = 12.8373 Debye
 Total < M_z > = 513.695 Debye

 Total < M_x^2 > = 2953.47 Debye^2
 Total < M_y^2 > = 164.796 Debye^2
 Total < M_z^2 > = 263883 Debye^2

 Total < |M|^2 > = 267001 Debye^2
 Total < |M| >^2 = 267001 Debye^2

 < |M|^2 > - < |M| >^2 = 0 Debye^2

Finite system Kirkwood g factor G_k = 0
Infinite system Kirkwood g factor g_k = 0

Epsilon = 1

The same structure (i.e., what i have used in the above command) if I open
and check for the dipole moment using YASARA suite of program it is showing
as 173 Debye. Which is reasonable. Am I making any mistake while obtaining
the dipole moment using g_dipoles or I am looking at the wrong file ??

Thanks.

Ram.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090316/21311f9d/attachment.html>