A tool for the automatic generation of interaction beads in a coarse-grained model of a macromolecule.

This tool, developed as part of a Research, Scholarship, and Creative Activities (RSCA) grant, is designed to provide a practical solution for overcoming the limitations of traditional multipole expansions in coarse-graining electrostatic potentials. It implements a novel distributed multipole expansion algorithm to accurately represent electrostatic potentials near the surfaces of biological molecules.

This tool integrates automatic geometric partitioning methods with Octree-based spatial structures to efficiently model biological molecules. Its algorithms handle data parsing, merging partitions, and the iterative reduction of molecular complexity while preserving essential properties. Creating coarse-grained models significantly improve computational efficiency, enabling large-scale simulations of complex biophysical systems.