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. SA
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