Hi. I am running simulations with DPPC and water molecules. I made groups from a set of atoms from each DPPC molecule (example: Group 1 = C1, C2, C3 Group 2 = C4, C5, C6). I want to calculate the rdf for the center of mass of each group from each DPPC molecule while excluding groups located on the same molecule. I am using the command line: g_rdf -n index -rdf res_com -s full -o rdf08SEPT106.xvg
I thought that I would have to edit my topology file to prevent the rdf from including groups on the same molecule, however, after editing my topology file my rdf does not change. By using the res_com option are groups with the same residue number automatically excluded from the rdf calculation? Emily
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