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: [email protected]
To: [email protected]
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 <[email protected]>
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.
[email protected] [email protected] http://folding.bmc.uu.se
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