[gmx-users] g_dipole ? => dipole moment ?
dommert at icp.uni-stuttgart.de
Sun Oct 17 15:31:15 CEST 2010
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On 10/16/2010 10:28 PM, David van der Spoel wrote:
> On 2010-10-16 21.36, Chih-Ying Lin wrote:
>> 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" ?
It is not a trivial task do determine the dielectric constant of a
system containing charged molecules. Many articles have been published
about this subject. The net-charge of a the molecule is subtracted at
the center of mass to decompose the dipole moment into a rotational and
translational part. I do not in what property of your system you are
exactly interested, but there is also the tool g_current which can
determine the rotational and translational part of the dipole moment.
>> 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
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
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