Ms. Anindita Gayen
C/O Dr. Chaitali Mukhopadhyay
Junior Research Fellow
Department of Chemistry
University of Calcutta
92, A. P. C. Road
Kolkata-700 009
India
--- On Fri, 9/5/08, ANINDITA GAYEN <[EMAIL PROTECTED]> wrote:
From: ANINDITA GAYEN <[EMAIL PROTECTED]>
Subject: Electron Density Across the Lipid Bilayer
To: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
Cc:
"[EMAIL PROTECTED]"
<[EMAIL PROTECTED]>, [EMAIL PROTECTED],
[EMAIL PROTECTED], [EMAIL PROTECTED],
[EMAIL PROTECTED], [EMAIL PROTECTED]
Date: Friday, 9 May, 2008, 5:57 PM
Dear Sir/Madam,
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:
g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm
where electrons.dat contains # of electrons for each and every atomtype defined in the system. 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.
I read from literature that i have to shift the z values with half of my box size.
However, I have used trjconv to center the bilayer inside the box by the command,
trjconv -f traj.trr -pbc nojump -o traj1.trr -s traj.tpr
trjconv -f traj1.trr -s traj.tpr -pbc whole -center rect -o centeredtraj.trr
and then used the g_density over the centeredtraj.trr
but the problem is again the g_density is calculating the electron density over the 50slices, that means no improvement.
Kindly suggest me as to how should I proceed,
I am eagerly waiting for your reply,
Anindita Gayen
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