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? 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 >
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