[gmx-users] g_dipoles

[rams rams]

Thank you Berk.

Is there any way I can draw some reasonable numbers out of it. My main
concern is to see the variation of the dipolemoment along the simulation
time.

Ram.

2009/3/17 Berk Hess <gmx3 at hotmail.com>

>  Hi,
>
> I don't think orientation is an issue.
>
> I guess the numbers could be correct.
> g_dipoles subtracts the net charge of a molecules at its center of mass.
> If your charge a located somewhat to one side of the molecule,
> this could result in a quite large dipole.
>
> But different definitions are possible for the dipole of a charged
> molecule.
>
> Berk
>
> ------------------------------
> Date: Tue, 17 Mar 2009 10:44:47 -0400
> Subject: Re: [gmx-users] g_dipoles
> From: rams.crux at gmail.com
> To: gmx-users at gromacs.org
>
>
> Dear David,
>
> The peptide is having a -ve charge of 3. Though the components might
> dependent upon the orientation but the average might be the same
> irrespective of the orientation I suppose.
>
> Ram.
>
> On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel <spoel at xray.bmc.uu.se
> > wrote:
>
> 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
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