[gmx-users] g_dipole
Carmen Domene
carmen.domene at bioch.ox.ac.uk
Thu Jun 12 16:02:01 CEST 2003
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
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