Widely available computing resources enable researchers to conduct multi-copy or ensemble based molecular dynamics studies that compare the structure and dynamics of 10's to 100's of different biomolecular complexes each containing hundreds of thousands of atoms. On a single GPU workstation, molecular dynamics compute engines now achieve over 100ns/day on systems containing 100,000 atoms. Supercomputing resources support the accumulation of microseconds of sampling overnight for systems containing, ∼250,000 atoms, such as explicit solvent models of the nucleosome. Nucleosomes, the fundamental building blocks of chromatin, affect all genomic processes and have a complexity of order 4147, thus tools to identify a nucleosome of interest, setup, and manage simulation and analysis tasks are needed to advance our understanding of multiscale genome organization. Here we introduce Nu-Dash, a Python based tool for molecular dynamics simulation studies of nucleosomes based on tools developed for our Interactive Chromatin Modeling webserver, ICM-Web, and our genome dashboard, G-Dash. Nu-Dash works in conjunction with VMD, Python, AmberTools, 3DNA and a MD compute engine (e.g. NAMD) to enable users to determine the unique features of nearly any realization of the nucleosome. Templates based on the 1.9Å resolution 1KX5 structure are provided for human, mouse and frog variants of the canonical nucleosome; however, any existing nucleosome structure can be used as a template, including snapshots from our TMB Library. Upon completion of the simulation tasks, Nu-Dash provides a uniform application of analysis, including DNA helical parameter analysis, so that different simulations can be easily compared. Combined with G-Dash, individual nucleosomes of interest can be identified on a genome wide scale and compared to the TMB Library for reference. Nu-Dash thus provides a comprehensive workflow for comparative all atom molecular dynamics studies of any realization of the nucleosome.