[gmx-users] dipole moment of a charged peptide

Erik Marklund erikm at xray.bmc.uu.se
Fri Apr 1 09:48:17 CEST 2011

Dommert Florian skrev 2011-04-01 09.45:
> On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
>> Hi,
>>     I have a long-chain peptide which has a net charge of  +5 . I was
>> wondering whether the g_dipole will give any reasonable dipole moment
>> for a molecule with a net charge. Is there any suggestion I should
>> follow regarding calculation of dipole-moment of a charged molecule .
>>   I found that in the manual it is mentioned that 'For molecules with a
>> net charge, the net charge is subtracted atcenter of mass of the
>> molecule.'.  I did not understand what it means. I am using
>> gromacs-4.0.7.
>> Sanku
> If you have a charged molecule the dipole moment is not unique, so you
> have to choose a reference point and this can be done by subtracting the
> net charge at this point. Write down the formula and rearange the terms
> and you will clearly see, what I mean.
> Cheers,
> Flo
And, if I recall correctly, there are two "natural" choices for this 
reference pont. One is the center of charge, the other is the center of 
mass. The latter is perhaps less intuitive, but better related to 
experimental observables.

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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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