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 <g...@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.c...@gmail.com > To: gmx-users@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 <sp...@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. > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > 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. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > ------------------------------ > What can you do with the new Windows Live? Find > out<http://www.microsoft.com/windows/windowslive/default.aspx> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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