Dear VOTCA users and developers, I have a problem in differentiating between intra- and inter-molecular non-bonded distributions: the system under consideration consists of 3 identical polymer chains, so normally one would need to provide a mapping for only one of those chains and the rest is cared by VOTCA. Unfortunately in this approach I haven't found a way to distinguish between similar beads for inter and intra-molecular non-bonded distributions. Let's say the bead A1 of the type A in the 1st chain is the reference bead and the bead A1 in the 3rd chain is the observable bead. What I want to look at is the distribution function A1_1st-A1_3rd, for example. Manipulation with the underlying atomistic PDB file by renaming atoms or fragments from different chains always gives mapping error when checking with csg_dump. If the naming in original PDB is identical in all 3 chains, introducing new bead types and names in mapping file always leads to mapping 3 different bead type into a single chain, not different ones. Is there a way to differentiate between different chains when calculating non-bonded distribution functions?
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