[gmx-users] g_dipoles output
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jun 14 21:14:21 CEST 2007
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
>> 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
> Is that correct?
> 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.
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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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