Hi According to the following website, http://en.wikipedia.org/wiki/Bond_dipole_moment
[image: \mu = \delta \, d]. The bond dipole is modeled as +δ -- δ- with a distance *d* between the partial charges <http://en.wikipedia.org/wiki/Partial_charges> +δ and δ-. For a complete molecule the total molecular dipole moment may be approximated as the vector sum of individual bond dipole moments. However, for a molecule of multiple atoms, There may be more than one bond connected on one atom. E | B - A - C partial charge of atom_A = -0.5 partial charge of atom_B = 0.2 partial charge of atom_C = 0.35 partial charge of atom_E = 0.4 Which partial charges should I use when I calculate bond-dipole-moment of A-B ? Which partial charges should I use when I calculate bond-dipole-moment of A-C ? Which partial charges should I use when I calculate bond-dipole-moment of A-E ? Thank you Lin 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" ? > > > > > >
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