[gmx-users] g_dipole ? => dipole moment ?
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 18 08:33:57 CEST 2010
On 2010-10-18 03.30, Chih-Ying Lin wrote:
> 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
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
> 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
> > 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
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