Thank you Berk.<br><br>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.<br><br>Ram.<br><br><div class="gmail_quote">2009/3/17 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
Hi,<br><br>I don't think orientation is an issue.<br><br>I guess the numbers could be correct.<br>g_dipoles subtracts the net charge of a molecules at its center of mass.<br>If your charge a located somewhat to one side of the molecule,<br>
this could result in a quite large dipole.<br><br>But different definitions are possible for the dipole of a charged molecule.<br><br>Berk<br><br><hr>Date: Tue, 17 Mar 2009 10:44:47 -0400<br>Subject: Re: [gmx-users] g_dipoles<br>
From: <a href="mailto:rams.crux@gmail.com" target="_blank">rams.crux@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><div><div></div><div class="h5"><br><br>Dear David,<br>
<br>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.<br><br>Ram.<br><br><div>
On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote style="padding-left: 1ex;">
<div><div></div><div>rams rams wrote:<br>
<blockquote style="padding-left: 1ex;">
Dear Users,<br>
<br>
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:<br>
<br>
g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg -n prot_dip.ndx<br>
<br>
I am giving the last few lines of the output below:<br>
<br>
Dipole moment (Debye)<br>
---------------------<br>
Average = 516.7213 Std. Dev. = 0.0000 Error = 0.0000<br>
<br>
The following averages for the complete trajectory have been calculated:<br>
<br>
Total < M_x > = -54.3459 Debye<br>
Total < M_y > = 12.8373 Debye<br>
Total < M_z > = 513.695 Debye<br>
<br>
Total < M_x^2 > = 2953.47 Debye^2<br>
Total < M_y^2 > = 164.796 Debye^2<br>
Total < M_z^2 > = 263883 Debye^2<br>
<br>
Total < |M|^2 > = 267001 Debye^2<br>
Total < |M| >^2 = 267001 Debye^2<br>
<br>
< |M|^2 > - < |M| >^2 = 0 Debye^2<br>
<br>
Finite system Kirkwood g factor G_k = 0<br>
Infinite system Kirkwood g factor g_k = 0<br>
<br>
Epsilon = 1<br>
<br>
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 ??<br>
</blockquote>
<br></div></div>
Is the peptide neutral? Otherwise the result might be orientation dependent.<br>
<br>
<br>
<blockquote style="padding-left: 1ex;">
<br>
Thanks.<br>
<br>
Ram.<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
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<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
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