ANINDITA GAYEN wrote:
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. *
The system is periodic, so you can happily subtract 30 from all the Z
values in the output yourself.
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.
Well you can be more confident that the middle Z value is the middle of
your bilayer, so that is an improvement.
Mark
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