[gmx-users] g_dipole

[David]

On Thu, 2003-06-12 at 18:40, Carmen Domene wrote:
> > Dipole moment (Debye)
> > ---------------------
> > Average  = 1101.3528  Std. Dev. = 151.9949  Error =  75.9975
> >
> > The following averages for the complete trajectory have been calculated:
> >
> >  Total < M_x > = 2758.17 Debye
> >  Total < M_y > = 2620.62 Debye
> >  Total < M_z > = 2073.38 Debye
> > This is what you want to look at: 1 Debye is roughly 48 e nm, so what
> > you have here (M_x) is roughly 56 e nm, or, if your protein is 2 nm,
> > this would correspond to +14 on one side and -14 on the other side. Is
> > it that much charged?
> 
> Sorry, but could you tell me the meaning of the Average value that comes
actually I don't know, check the source it's quite easy.

> from g_dipole and also how you calculate the dipole of a charged system
> with g_dipole? Do you calculate the dipole wrt the center of mass of the
> system, a geometrical center or maybe something else?
We don't take a total charge into account, you just get sum q r, if you
want to know with respect to the center of mass, use editconf to center
your molecule at the origin. Of course as long as you have a charge it
is still arbitrary. You could try to center the protein at the center of
charge, i.e. take the dipole above, divide by twelve* 48  and move the
molecule along that vector in the opposite direction..


> My protein has a total charge of +12.
> 
> Thanks, Carmen
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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