Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters

Macromolecular assemblies often display a hierarchical organization of macromolecules or their subassemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100 ns, 2 million atom solvated human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the <i>N</i>-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field-based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure.