On 2010-10-18 03.30, Chih-Ying Lin wrote:
HI
I confined one molecule in the center of box and issue the g_dipole command.
The average dipole moment is still around 32.
It is the molecule with 33 atoms / united atoms of most carbon groups,
isn't the dipole moment around 32 too high?
How can I test next and know that the dipole moment around 32 is
acceptable?
By calculating on paper: dipole is 48.0 sum of q_i x_i, therefore if you
have large charge separation you will get a large dipole.
Thank you
Lin
On 2010-10-16 21.36, Chih-Ying Lin wrote:
>
> Hi
> I issue the g_dipole command on Gromacs => And, the following
> information is shown.
> There are 10 molecules in the selection,
> Does the Average =32.1611 refer to the average for a single over the
> simulation time?
> Or, the Average = 32.1611 summing for all the 10 molecules over the
> simulation time?
> If the average = 32.1611 for a single molecule with 33 atoms / united
> atoms of most carbon groups, isn't the dipole moment too high?
I think this is the average per molecule. You may need to run trjconv
-pbc whole, because mdrun may break molecules in two parts, meaning that
the molecule becomes as big as the box.
>
>
>
>
> What does "will subtract their charge at their center of mass" this
mean?
> Why "will subtract their charge at their center of mass" ?
>
>
>
>
> ==================================================================
> There are 10 molecules in the selection
> There are 10 charged molecules in the selection,
> will subtract their charge at their center of mass
> Using Volume from topology: 220.317 nm^3
>
> Back Off! I just backed up epsilon.xvg to ./#epsilon.xvg.1#
>
> Back Off! I just backed up aver.xvg to ./#aver.xvg.1#
> Last frame 10000 time 20000.000
> Average volume over run is 221.043
>
> Dipole moment (Debye)
> ---------------------
> Average = 32.1161 Std. Dev. = 2.9926 Error = 0.0095
>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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