[gmx-users] g_dipole

[Carmen Domene]

Hi.

I am trying to calculate the dipole moment of a protein (which is
charged).

I am not sure whether I fully understand the output from g_dipole.
May I get any help, please?

For the protein itself using a pdb file as input (not a trajectory),
I get the following output:

***************************************************************************
Dipole moment (Debye)
---------------------
Average  = 1101.3528  Std. Dev. = 151.9949  Error =  75.9975

The following averages for the complete trajectory have been calculated:

 Total < M_x > = 2758.17 Debye
 Total < M_y > = 2620.62 Debye
 Total < M_z > = 2073.38 Debye

 Total < M_x^2 > = 7.60751e+06 Debye^2
 Total < M_y^2 > = 6.86763e+06 Debye^2
 Total < M_z^2 > = 4.29889e+06 Debye^2

 Total < |M|^2 > = 1.8774e+07 Debye^2
 Total < |M| >^2 = 1.8774e+07 Debye^2

 < |M|^2 > - < |M| >^2 = -9.31323e-10 Debye^2

Finite system Kirkwood g factor G_k = -1.9195e-16
Infinite system Kirkwood g factor g_k = -1.9195e-16

Epsilon = 1
****************************************************************************

If I do:   sqrt((M_x)^2+(M_y)^2+(M_z)^2) using the number above,
I do not get anything similar to Average  = 1101.3528 (even if I consider
the error).

As the system is charged and the dipole is origen dependent in this case,
is Average the final value calculated wrt the center of mass of the
protein?

When I use g_dipole with a water molecule things look better:

*****************************************************************************
Dipole moment (Debye)
---------------------
Average  =   2.2678  Std. Dev. =   0.0000  Error =   0.0000

The following averages for the complete trajectory have been calculated:

 Total < M_x > = 1.35882 Debye
 Total < M_y > = 0.393859 Debye
 Total < M_z > = 1.77238 Debye

 Total < M_x^2 > = 1.84639 Debye^2
 Total < M_y^2 > = 0.155125 Debye^2
 Total < M_z^2 > = 3.14132 Debye^2

 Total < |M|^2 > = 5.14284 Debye^2
 Total < |M| >^2 = 5.14284 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
**************************************************************************

so that now:       sqrt((M_x)^2+(M_y)^2+(M_z)^2) =  Average

I have also tried using a system with two K ions but I get:

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

The following averages for the complete trajectory have been calculated:

 Total < M_x > = 0 Debye
 Total < M_y > = 0 Debye
 Total < M_z > = 0 Debye

 Total < M_x^2 > = 0 Debye^2
 Total < M_y^2 > = 0 Debye^2
 Total < M_z^2 > = 0 Debye^2

 Total < |M|^2 > = 0 Debye^2
 Total < |M| >^2 = 0 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
****************************************************************************

and I do not know why.

Many thanks.

Best wishes,

Carmen