[gmx-users] g_dipole

[David]

On Thu, 2003-06-12 at 16:01, Carmen Domene wrote:
> Hi.
> 
> I am trying to calculate the dipole moment of a protein (which is
> charged).
> 
> I am not sure whether I fully understand the output from g_dipole.
> May I get any help, please?
> 
> For the protein itself using a pdb file as input (not a trajectory),
> I get the following output:
> 
> ***************************************************************************
> 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?


-- 
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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