[gmx-users] res_com in g_rdf

Emily Curtis emilymariecurtis at gmail.com
Thu Sep 9 21:18:26 CEST 2010

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?

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