[gmx-users] Values of radial density profiles

sa sagmx.mail at gmail.com
Fri Feb 25 15:17:28 CET 2011

Dear All

 I would like to compute the radial density function rho(r) (in g/cm3) of
different parts of micelle formed with DPC molecules (such as headgroup,
alkyl tail and water) relative to the center of mass of the aggregate. I
have constructed an index files containing all the atoms of the surfactant
headgroup and alkyl chain and used g_rdf (4.5.3):

 /work/cont003/abel01/gmx4.5.3/bin/g_rdf_mpi -f *_Center_All.xtc -s
run_1.tpr -o DPC-Self-AMB_100-155ns_HEADGROUP_RDF.xvg -b 100000 -e 155000
-norm -com -n index_Radial_Profile_DPC.ndx

 For water, as expected, I obtained a RDF profile where rho (r) values tend
to the water density (~1g/cm3) near the simulation  edge  box.  For the
headgroup and the alkyl tail of the DPC, it is not the case since I obtained
two peaks with rho (r) values higher than the density a phosphocholine group
and a dodecyl alkyl chain (in my case 26.4 and 16.4 ).

 What is wrong with command used above. Did i forget something ?

 Thank you in advance for your help.

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