[gmx-users] g_dipole ? => dipole moment ?

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se