Pure FENE Bond Potential for Soft Matter and Biological Simulations: Theory, HOOMD-blue Implementation, and Applications to Polymer, Colloidal, and Membrane Systems

Abstract

The finitely extensible nonlinear elastic (FENE) potential is widely used as a bonded interaction in coarse-grained simulations of polymers, soft matter, colloids, and biological systems. In the classical Kremer--Grest framework, FENE bonding is combined with a short-range Weeks--Chandler--Andersen (WCA) interaction to provide finite bond extensibility together with excluded-volume repulsion. Although this combination is highly successful, it intrinsically couples bonded elasticity to the nonbonded interaction, limiting the ability to independently control these two contributions. Here, we introduce a standalone FENE bond potential in HOOMD-blue in which finite bond extensibility is implemented independently of the choice of nonbonded interaction. This formulation allows the same FENE bond potential to be combined with WCA, Lennard--Jones, or other pair interactions without modifying the bonded interaction itself. We demonstrate the utility of the standalone formulation in coarse-grained polymer chains, colloidal networks, and mesh-based biological membrane models. Across these systems, Pure FENE bonding without short-range excluded-volume stabilization produces pronounced structural contraction, whereas the addition of WCA repulsion suppresses this collapse and preserves finite, spatially extended structures. These results demonstrate that separating finite bond extensibility from steric interactions provides independent control over local bond mechanics and collective structural organization. The standalone FENE formulation therefore provides a modular framework for coarse-grained simulations in which molecular connectivity and nonbonded interactions represent distinct physical mechanisms.