[gmx-users] g_dipoles

[David van der Spoel]

rams rams wrote:
> Dear Users,
> 
> I am trying to obtain the dipole moment of a 40 amino acid residue 
> peptide using g_dipoles. I am getting a huge number (about 700 Debye). I 
> expect it to be around 150 Debye (based on other studies). To make sure 
> it I extracted a shapshot of the structure and obtained the dipolemoment 
> using the following command:
> 
> g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg  -n prot_dip.ndx
> 
> I am giving the last few lines of the output below:
> 
> Dipole moment (Debye)
> ---------------------
> Average  = 516.7213  Std. Dev. =   0.0000  Error =   0.0000
> 
> The following averages for the complete trajectory have been calculated:
> 
>  Total < M_x > = -54.3459 Debye
>  Total < M_y > = 12.8373 Debye
>  Total < M_z > = 513.695 Debye
> 
>  Total < M_x^2 > = 2953.47 Debye^2
>  Total < M_y^2 > = 164.796 Debye^2
>  Total < M_z^2 > = 263883 Debye^2
> 
>  Total < |M|^2 > = 267001 Debye^2
>  Total < |M| >^2 = 267001 Debye^2
> 
>  < |M|^2 > - < |M| >^2 = 0 Debye^2
> 
> Finite system Kirkwood g factor G_k = 0
> Infinite system Kirkwood g factor g_k = 0
> 
> Epsilon = 1
> 
> The same structure (i.e., what i have used in the above command) if I 
> open and check for the dipole moment using YASARA suite of program it is 
> showing as 173 Debye. Which is reasonable. Am I making any mistake while 
> obtaining the dipole moment using g_dipoles or I am looking at the wrong 
> file ??

Is the peptide neutral? Otherwise the result might be orientation 
dependent.


> 
> Thanks.
> 
> Ram.
> 
> 
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> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se