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

[David van der Spoel]

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