[gmx-users] density profile of bilayers

Zoltan Varga vargaz_137 at yahoo.com
Wed Oct 17 09:18:51 CEST 2007


priyanka srivastava <priyankaps4 at yahoo.com> 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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