[gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf.

[sa]

Dear GMXusers,

Last week, i asked a question about the calculation of average radial
density functions relative to the center of mass of a micelle formed with
DPC molecules (rdf). Unfortunately i received no response. So i re ask my
question. So I would like to obtain the average rdf function (in g/cm3) for
different groups of my micellar system (such as the headgroup, alkyl tail of
the surfactant and water). For this purpose, I have created a index file
where all DPC atoms (heavy and H atoms ) are separated in different groups
and use the following command with g_rdf (4.5.3)

g_rdf_mpi -f *_Center_All.xtc -s run_1.tpr -o
DPC-Self-AMB_100-155ns_DPC_RDF.xvg -b 100000 -e 155000 -norm -com -n
index_Radial_Profile_DPC.ndx

I chose DPC atoms as a reference group and obtain the rdf curves for the DPC
headgroup, alkyl tail and water. I obtain the following figure :

http://img4.hostingpics.net/pics/213680DPCSelfAMB100155nsRDF.jpg

I don't understand why the curves amplitudes for the headgroup, alkyl tail
are so high (and what is the unity ?),  For example for the C12 alkyl chain
rdf  I understand well the help of the g_rdf tool, I expect a rdf with a
density maxima around 0.8 - 0.9 g/cm3. Did i compute the expected function
with above command ? If not, how to obtain the rdf (in g/cm3) for each
components ?

Thanks for the help.

SA
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