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

[Florian Dommert]

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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:
>>
>> 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"  ?
>>

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.

/Flo


>>
>>
>>
>> ==================================================================
>> 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
>>
> 
> 


- -- 
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
Fax:   +49-(0)711/685-6-3658

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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