<table cellspacing='0' cellpadding='0' border='0' ><tr><td style='font: inherit;'><br><br>Ms. Anindita Gayen<br>
C/O Dr. Chaitali Mukhopadhyay<br>
Junior Research Fellow<br>
Department of Chemistry<br>
University of Calcutta<br>
92, A. P. C. Road<br>
Kolkata-700 009<br>
India<br><br>--- On <b>Fri, 9/5/08, ANINDITA GAYEN <i><aninditagayen@yahoo.co.in></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">From: ANINDITA GAYEN <aninditagayen@yahoo.co.in><br>Subject: Electron Density Across the Lipid Bilayer<br>To: "vargaz_137@yahoo.com" <vargaz_137@yahoo.com><br>Cc:
"dallas.warren@vcp.monash.edu.au"
<dallas.warren@vcp.monash.edu.au>, tieleman@ucalgary.ca,
Xavier.Periole@physbio.mssm.edu, priyankakaps4@yahoo.com,
spoel@xray.bmc.uu.se, Mark.Abraham@anu.edu.au<br>Date: Friday, 9 May, 2008, 5:57 PM<br><br><div id="yiv678400301"><table cellspacing="0" cellpadding="0" border="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-stretch: inherit; font-size-adjust: inherit;"><div id="yiv179437194">
<div> </div>
<div>Dear Sir/Madam,</div>
<div><br>I wish to calculate the density profile of a DMPC lipid
bilayer i.e the electron density and for this I am using the g_density
command:<br><br><font size="3">g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm <br></font>where electrons.dat contains # of electrons for each and every atomtype defined in the system. <strong>However
it reports electron density for 50slices (setup by -sl) which ranges
from 0 to 60. while I want it to vary from, -30 to +30. </strong></div>
<div><br>I read from literature that i have to shift the z values with half of my box size. <br><br>However, I have used trjconv to center the bilayer inside the box by the command,</div>
<div><font size="3">trjconv -f traj.trr -pbc nojump -o traj1.trr -s traj.tpr</font></div>
<div><font size="3">trjconv -f traj1.trr -s traj.tpr -pbc whole -center rect -o centeredtraj.trr</font></div>
<div> </div>
<div>and then used the g_density over the centeredtraj.trr </div>
<div>but the problem is again the g_density is calculating the electron density over the 50slices, that means no improvement.</div>
<div> </div>
<div>Kindly suggest me as to how should I proceed,<br>I am eagerly waiting for your reply,</div>
<div><br>Anindita Gayen</div></div></td></tr></tbody></table><br>
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