[gmx-users] Fw: Electron Density Across the Lipid Bilayer

[Mark Abraham]

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