Automatic Generation of the Interaction Beads of a Distributed Multipole Analysis Model of a Macromolecule

Multipole expansions (MEs) provide a natural path toward a scale-adjustable strategy for coarse-graining (CG) the electrostatic field of a distribution of charge. Such a strategy is of special importance, for example, in the molecular dynamics simulation of biological systems. The main limitation of the MEs is their convergence requirements: convergence is guaranteed only outside a spherical enclosure of the distribution of charge. For systems such as biological molecules this is a serious limitation since the region of interest is, typically, in the immediate vicinity of the molecular surface where the requirement is not readily satisfied. The solution is to partition the distribution of charge into subsets, and use separate multipole expansion for each subset; i.e. a Distributed Multipole Analysis (DMA).

In previous work we developed an algorithm for the automatic partitioning of a charge distribution into components (CG beads) such that the convergence of the DMA is satisfied at specified locations around the distribution of charge. In this presentation we report on a software tool that we developed to implement that algorithm. We also report results that illustrate the performance of the tool, and potential additional optimizations that these results suggest in the case of protein molecules.