[gmx-users] g_dipoles output

[David van der Spoel]

Martin Höfling wrote:
> Hi Folks, 
> 
> I struggle with the output of g_dipoles, just to make sure that I understood 
> it right:
> 
> I select a subpart of my simulation and get the following output:
> 
>> Average volume over run is 216
>>
>> Dipole moment (Debye)
>> ---------------------
>> Average  =   0.4463  Std. Dev. =   0.5010  Error =   0.0003

average dipole per molecule

> 
> Is this the dipole moment of my group normalized to the volume? I especially 
> do not understand the difference between this value and the following ones.
volume does not enter these values at all.

> 
>> The following averages for the complete trajectory have been calculated:
>>
>>  Total < M_x > = -2.20102 Debye
>>  Total < M_y > = -1.65231 Debye
>>  Total < M_z > = -2.24414 Debye
> 
> OK these are the component average values over time from dipole moment of my 
> group.
> 
>>  Total < M_x^2 > = 1200.66 Debye^2
>>  Total < M_y^2 > = 1200.07 Debye^2
>>  Total < M_z^2 > = 1252.29 Debye^2
> 
> Average deviation from zero (squared) from each component over time.
> 
>>  Total < |M|^2 > = 3653.02 Debye^2
> 
> Same thing for total Dipole momentum.
> 
>>  Total < |M| >^2 = 12.6108 Debye^2
> 
> Average orientation (squared) of the total dipole momentum of my group over 
> time.
> 
> Is that correct?
yes.

> Ok, now if i g_analyze -f Mtot.xvg -ee
> 
>> Read 4 sets of 1001 points, dt = 5
>>
>>                                       std. dev.    relative deviation of
>>                        standard       ---------   cumulants from those of
>> set      average       deviation      sqrt(n-1)   a Gaussian distribition
>>                                                       cum. 3   cum. 4
>> SS1  -2.201018e+00   3.458052e+01   1.093532e+00      -0.114    0.021
>> SS2  -1.652311e+00   3.460259e+01   1.094230e+00       0.016   -0.018
>> SS3  -2.244139e+00   3.531650e+01   1.116806e+00      -0.004    0.008
>> SS4   5.565348e+01   2.357344e+01   7.454575e-01       0.332   -0.002
> 
> Hmm, these values in the first column deviate from the (sqrt) of the above 
> ones for the components and total one.
because you have only the values in the xvg file, while the edr file 
stores more statistics.

> 
> Thanks for any comments.
> 
> Btw, in the 3.3 manual, e*nm is stated as dipole moment unit. I checked the 
> sourcecode of g_dipoles and afair, the units there are still in Debye.
yes it's debye, because that is what people understand. should update 
the manual than.

> 
> Cheers
> 	Martin
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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