I am attempting to output the radial distribution function for a simulation and am using the fix rdf command. I would like to only output the intermolecular rdf and exclude the counting of any atoms within the same molecule. The documentation states that I can avoid counting any bonded atoms (1-2, 1-3, 1-4 interactions within a molecular topology) by using the command “special_bonds 0.0 0.0 0.0”. However, when I do this, the rdf’s are still counting the bonded atoms and are washing out all of the intermolecular data that I am interested in.
Is anyone familiar with using this fix command? Is my interpretation of the “special_bonds” command correct in that if you set the values to 0.0, LAMMPS will not include those bonded atoms when creating the rdf? Are there any other ways, such as post-processing, that have been implemented for computing rdf’s?
I am using the 10Nov05 LAMMPS version for this work. I have attached my input file for reference.
boundary p p p