[gmx-users] mass density

Dinesh Pinisetty dpinis1 at lsu.edu
Wed Mar 2 07:33:47 CET 2005

Hello everybody,
        I want to analyze lipid/water/alcohol system.I have following
1) Does g_density give mass density profiles.
If we use g_density -f traj.xtc -s topol.tpr -n index.ndx -o density.xvg
and if we select residue name of alcohol,does this give mass density
profile of the alcohol.

2) How to get the orientation of the water dipole,I mean a graph of mean
cosine angle of water dipole and bilayer normal.Does any of the commands
directly give the cosine function values.

3) I have created an index.ndx file such that I had [sn-1] and [sn-2] tails
in it.I want to look at the order parameter of sn-1 and sn-2.When I used
g_order its giving me error saying that gr1 atoms does not match with gr1
atoms.Is there any specific way to prepare an index file for finding order
parameter using g_order.

 Any suggestions would be greatly appreciated.
Thanking you,
Yours sincerely,

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