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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