[gmx-users] Density Profile

afsaneh maleki maleki.afsaneh at gmail.com
Thu Jan 7 11:38:01 CET 2010


 I obtained the electron density profile for the solvent in protein membrane

For this I used the following commands:

 ]$ g_density  -f md.xtc  -s md.tpr  -d  z  -dens electron   -o sol.xvg   -ei
electrons.dat   -symm

-n index.ndx

  Although in md.gro file is seen any water in middle box (hydrophobic
region) simulation, Plot shows the electron density of the water is higher
in the middle bilayer  than the edges.

Would any help me to remove this problem?

are commands used correctly?

Best regards,
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