[gmx-users] g_dipoles

[Berk Hess]

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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-- 

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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