Hello,
priyanka srivastava <[EMAIL PROTECTED]> wrote: Dear all,
I wish to calculate the density profile of a lipid bilayer i.e the electron
density and this is how 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 e.g.
C2A = 6
NTM = 7
OA = 8 etc....
However it reports electron density for 50bins (setup by -sl) which ranges from
0 to 50. However I want it to vary from, -30 to +30.
Maybe I'm wrong, but it reports the electron density along the z axis of the
box with a grid what contains 50 bins. So to get an electron density which
ranges from -30 to +30 (in Angstroms and with the bilayer center at 0, I guess)
you should only shift the z values with half of your box size.
Another point is, I want the density profile separately for P, N, acyl, water
etc. Should I define a separate electrons.dat for this purpose?
No, you should make an index file for that which contains P, N, etc. groups and
run g_density -n new_index.ndx ...
Kindly suggest me as to how should I proceed,
eagerly waiting for your reply,
Priyanka S...
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Hope that helped,
Zoltan Varga
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