[lammps-users] Question about computing RDFs for coarse-beads/super-atoms

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Hello,

I am using the LAMMPS (3 Mar 2020). I have built an all-atoms model of a polymer. I am trying to build a coarse-grained structure (coarse-beads/ super-atoms using clusters of explicit atoms) of the same polymer using the atomistic model. I have decided on the atoms clusters. I plan to use the trajectory of the centers of mass of the clusters to determine the bonded interaction potential parameters. I have used ‘com/chunk’ for that purpose. Now for the non-bonded interaction potential parameters, I need RDF for the centers of mass. In the documentation, I learned that ‘compute rdf’ can be used for that, but the command uses ‘atom type’ in its definition; whereas a typical coarse-bead/ super-atom contains more than 1 atom type. My question is :
Is there way to compute RDFs for coarse-grains?
Please let me know if you need any further information. Thank you very much.

With best wishes,
Arunjyoti Sinha Roy.

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what you want to do is best done in post processing, i.e. compute the center of mass trajectory and then compute the g® from that.

please note that LAMMPS includes a package for generating parameters for a specific coarse-graining approach: https://docs.lammps.org/Packages_details.html#pkg-mscg
that is probably not the model you have in mind, but worth a consideration in case your approach does not yield the expected results or has additional technical challenges.

axel.