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Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessibleto fine grain (FG) MD simulations. A CG simulation decreases the degrees offreedom by mapping atoms from an FG representation into agglomerate CGparticles. The FG to CG mapping is not unique. Research into systematicselection of these mappings is challenging due to their combinatorial growthwith respect to the number of atoms in a molecule. Here we present a method ofreducing the total count of mappings by imposing molecular topology andsymmetry constraints. The count reduction is illustrated by considering allmappings for nearly 49,889 molecules. The resulting number of mapping operatorsis still large, so we introduce hierarchical graphs which encode multiple CGmapping operators. The encoding method is demonstrated for methanol and a14-mer peptide. This encoding provides a foundation to perform automatedmapping selection.

Encoding and Selecting Coarse-Grain Mapping Operators with Hierarchical Graphs