http://matdl.org/matdlwiki/index.php/softmatter:Radial_Distribution_Func tion
That tells you what a rdf is and what the units are. It is a probability function, so your graph is saying that you are 25 times more likely to find the tails 1 nm from the center versus in the bulk. If you want a density, then you are going to have to do some subsequent processing to the data that the g_rdf script provides you. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of sa Sent: Tuesday, 1 March 2011 6:11 AM To: [email protected] Subject: [gmx-users] How to obtain the average radial density functions relative to the center of mass with g_rdf. 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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