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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
